# loading packages
pacman::p_load(tidyverse, # tidy family and related pacakges below
kableExtra,
gridExtra,
purrr,
magrittr, # extending piping
pander, # nice tables
metafor, # package for meta-analysis
MCMCglmm, # Bayeisan mixed model package
ggbeeswarm, # making bee-swarm plots possible
plotly # interactive plots using ggplot2
#mi, # missing data analysis
#betareg # dependance of the above
)
# getting functions
source("../R/ESM_functions.R", chdir = TRUE)
NOTE!!! We have XX custum functions: …….
Below is the dataset used for our meta-analysis follwed by explanations of 24 variables original collected (not all varaibles were used for our analyses; variables which were neither ‘directly’ nor ‘indirectly’ used in our analyses are indicated by *)
# getting the data and formating some variables (turning chraracter vectors
# to factors) read the difference between factr() and as.factor()
# <https://stackoverflow.com/questions/39279238/why-use-as-factor-instead-of-just-factor>
# full_data <- read.csv('../data/2019-04-04-source-data-dat.csv', na = 'NA',
# fileEncoding='UTF-8') %>% mutate_if(is.character, as.factor)
full_data <- read_csv("../data/2019-23-07-source-data-dat.csv", na = "NA") %>%
mutate_if(is.character, as.factor)
# making a scrollable table
kable(full_data, "html") %>% kable_styling("striped", position = "left") %>%
scroll_box(width = "100%", height = "500px")
| authors | year | host_tax_broad | host_tax_fine | symbiont_tax_broad | symbiont_tax_fine | symbiont_euk | symbiosis | endo_or_ecto | mode_of_transmission_broad | mode_of_transmission_fine | symbiont | Visiting_symbiont? | host_tips_linked | host_tips_linked_corrected | host_genera | total_host_symbioint_links | host_range_link_ratio | host_range_taxonomic_breadth | symbiont_tips_linked | symbiont_genera | no_randomizations | p_value | method |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Xu_et_al_2017 | 2017 | Invert | Invert | Microbe | Bacterium | n | Mutualist | Endo | vertical | vertical | Buchnera | resident | 20 | 20 | 8 | 20 | 1.00 | 1.00 | 20 | 1 | 1000 | 0.00100 | TreeMap |
| Riess_et_al_2018 | 2018 | Plant | Fungus | Microbe | Fungus | y | Parasite | Endo | horizontal | autonomous | Root fungus | resident | 11 | 11 | 5 | 11 | 1.00 | 1.00 | 11 | 2 | 1000 | 0.33500 | TreeMap |
| Badets_et_al_2011 | 2011 | Vert | Tetrapod | Invert | Invert | y | Parasite | Endo | horizontal | autonomous | Monogenea | resident | 17 | 17 | 13 | 17 | 1.00 | 1.00 | 17 | 4 | 1000 | 0.01000 | TreeMap |
| Banks_et_al_2006 | 2006 | Vert | Bird | Invert | Invert | y | Parasite | Ecto | both | contact | Chewing lice | resident | 18 | 18 | 6 | 30 | 2.00 | 1.60 | 15 | 2 | 1000 | 0.01000 | TreeMap |
| Bochkov_et_al_2011 | 2011 | Vert | Tetrapod | Invert | Invert | y | Parasite | Ecto | both | contact | Mites | resident | 6 | 6 | NA | 9 | 1.00 | 1.00 | 9 | 6 | 100 | 0.01000 | TreeMap |
| Charleston_&_Perkins_2003 | 2003 | Vert | Tetrapod | Microbe | Protist | y | Parasite | Endo | horizontal | vector | Malaria | resident | 9 | 9 | 1 | 9 | 1.00 | 1.00 | 9 | 1 | 100 | 0.03000 | TreeMap |
| Charleston_&_Robertson_2002 | 2002 | Vert | Tetrapod | Microbe | Virus | n | Parasite | Endo | horizontal | bodily fluid | Retrovirus | resident | 12 | 12 | 12 | 12 | 1.00 | 1.00 | 12 | 1 | 1000 | 0.01500 | TreeMap |
| Chauvatcharin_et_al_2006 | 2006 | Microbe | Bacterium | Microbe | Virus | n | Parasite | Endo | both | NA | Bacteriophage | resident | 14 | 14 | 7 | 15 | 1.07 | 1.00 | 14 | 1 | 1000 | 0.33100 | TreeMap |
| Clark_et_al_2000 | 2000 | Invert | Invert | Microbe | Bacterium | n | Mutualist | Endo | vertical | vertical | Buchnera | resident | 17 | 17 | 4 | 17 | 1.00 | 1.00 | 17 | 1 | 1000 | 0.00100 | TreeMap |
| Clayton_&_Johnson_2003 | 2003 | Vert | Bird | Invert | Invert | y | Parasite | Ecto | both | contact | Dove body lice | resident | 13 | 13 | 6 | 14 | 1.08 | 1.15 | 13 | 1 | 10000 | 0.00060 | TreeMap |
| Clayton_&_Johnson_2003 | 2003 | Vert | Bird | Invert | Invert | y | Parasite | Ecto | both | contact | Dove wing lice | resident | 13 | 13 | 6 | 16 | 1.60 | 1.50 | 10 | 1 | 10000 | 0.15300 | TreeMap |
| Cui_et_al_2012 | 2012 | Vert | Tetrapod | Microbe | Virus | n | Parasite | Endo | horizontal | bodily fluid | Retrovirus | resident | 7 | 7 | 3 | 7 | 1.00 | 1.00 | 7 | 7 | 10000 | 0.36600 | TreeMap |
| Dabert_2001__ | 2001 | Vert | Bird | Invert | Invert | y | Parasite | Ecto | both | contact | Feather mite | resident | 21 | 21 | 12 | 22 | 1.00 | 1.00 | 22 | 9 | 10000 | 0.00100 | TreeMap |
| Deng_et_al_2013 | 2013 | Invert | Invert | Invert | Invert | y | Parasite | Endo | horizontal | autonomous | Parasitic wasps | resident | 7 | 7 | 4 | 10 | 1.00 | 1.43 | 10 | 2 | 999 | 0.53000 | TreeMap |
| Desai_et_al_2010 | 2010 | Microbe | Protist | Microbe | Bacterium | n | Mutualist | Ecto | both | contact | Devescovinid flagellates | resident | 9 | 9 | 2 | 8 | 0.89 | 1.00 | 9 | 1 | 1000 | 0.00100 | TreeMap |
| Desdevises_et_al_2002 | 2002 | Vert | Fish | Invert | Invert | y | Parasite | Ecto | horizontal | autonomous | Monogenea | resident | 14 | 14 | 11 | 39 | 1.95 | 1.45 | 20 | 2 | 999 | 0.31700 | TreeMap |
| Downie_&_Gullan_2005 | 2005 | Invert | Invert | Microbe | Bacterium | n | Mutualist | Endo | vertical | vertical | Primary endosymbiont Tremblaya | resident | 21 | 21 | 16 | 21 | 1.00 | 1.00 | 21 | 1 | 1000 | 0.00100 | TreeMap |
| Erpenbeck_et_al_2002 | 2002 | Invert | Invert | Microbe | Bacterium | n | Mutualist | Endo | vertical | vertical | Sponge symbiont | resident | 6 | 6 | 5 | 6 | 1.00 | 1.00 | 6 | 1 | 10000 | 0.02000 | TreeMap |
| Etherington_et_al_2006 | 2006 | Vert | Tetrapod | Microbe | Virus | n | Parasite | Endo | horizontal | contact | Calicivirus | resident | 7 | 7 | 7 | 8 | 1.00 | 1.00 | 8 | 1 | 1000 | 0.01000 | TreeMap |
| Farrell_1998 | 1998 | Plant | Plant | Invert | Invert | y | Parasite | Ecto | horizontal | autonomous | Cerambicid beetle | resident | 21 | 21 | 2 | 21 | 1.00 | 1.00 | 21 | 6 | 1000 | 0.07000 | TreeMap |
| Gottschling_et_al_2011 | 2011 | Vert | Tetrapod | Microbe | Virus | n | Parasite | Endo | horizontal | contact | Papillomavirus | resident | 43 | 43 | 40 | 78 | 1.00 | 1.00 | 78 | 30 | 1000 | 0.00100 | TreeMap |
| Hendricks_et_al_2013 | 2013 | Vert | Bird | Invert | Invert | y | Parasite | Ecto | both | contact | Quill mites | resident | 19 | 19 | 17 | 20 | 1.25 | 1.25 | 16 | 1 | 1000 | 0.02100 | TreeMap |
| Hosokawa_et_al_2006 | 2006 | Invert | Invert | Microbe | Bacterium | n | Mutualist | Endo | vertical | vertical | Gamma proteobacteria | resident | 7 | 7 | 3 | 7 | 1.00 | 1.00 | 7 | 1 | 1000 | 0.00100 | TreeMap |
| Hugot_1999 | 1999 | Vert | Tetrapod | Invert | Invert | y | Parasite | Endo | horizontal | trophic | Pinworms | resident | 10 | 10 | 9 | 11 | 1.00 | 1.00 | 11 | 6 | 1000 | 0.00100 | TreeMap |
| Hugot_et_al_2003 | 2003 | Vert | Tetrapod | Microbe | Fungus | y | Parasite | Endo | horizontal | contact | Pneumocystis | resident | 19 | 19 | 12 | 19 | 1.00 | 1.00 | 19 | 1 | 1000 | 0.00100 | TreeMap |
| Huyse_&_Volckaert_2005 | 2005 | Vert | Fish | Invert | Invert | y | Parasite | Ecto | horizontal | autonomous | Gyrodactylus flatworms | resident | 8 | 8 | 3 | 22 | 1.29 | 1.24 | 17 | 1 | 100 | 0.02000 | TreeMap |
| IkedaOhtsubo_&_Brune_2009 | 2009 | Microbe | Protist | Microbe | Bacterium | n | Mutualist | Ecto | vertical | vertical | Endomicrobium | resident | 11 | 11 | 1 | 11 | 1.00 | 1.00 | 11 | 1 | 1000 | 0.00100 | TreeMap |
| Jackson_&_Charleston_1994 | 1994 | Vert | Tetrapod | Microbe | Virus | n | Parasite | Endo | horizontal | contact | Lyssavirus | resident | 10 | 10 | 8 | 10 | 1.00 | 1.00 | 10 | 1 | 100 | 0.19000 | TreeMap |
| Jackson_&_Charleston_1994 | 1994 | Vert | Tetrapod | Microbe | Virus | n | Parasite | Endo | horizontal | bodily fluid | Retrovirus | resident | 10 | 10 | 7 | 10 | 1.00 | 1.00 | 10 | 1 | 100 | 0.01000 | TreeMap |
| Jackson_&_Charleston_1994 | 1994 | Vert | Tetrapod | Microbe | Virus | n | Parasite | Endo | horizontal | contact | Arenavirus | resident | 11 | 11 | 7 | 12 | 1.00 | 1.00 | 12 | 1 | 100 | 0.05000 | TreeMap |
| Jackson_&_Charleston_1994 | 1994 | Vert | Bird | Microbe | Virus | n | Parasite | Endo | horizontal | bodily fluid | Retrovirus | resident | 13 | 13 | 9 | 15 | 1.00 | 1.00 | 15 | 1 | 100 | 0.18000 | TreeMap |
| Jackson_&_Charleston_1994 | 1994 | Vert | Tetrapod | Microbe | Virus | n | Parasite | Endo | horizontal | contact | Hantavirus | resident | 14 | 14 | 7 | 17 | 1.00 | 1.00 | 17 | 1 | 100 | 0.01000 | TreeMap |
| Jeong_et_al_1999 | 1999 | Plant | Plant | Microbe | Bacterium | n | Mutualist | Endo | horizontal | vector | Frankia | resident | 12 | 12 | 12 | 19 | 1.06 | 1.00 | 18 | 1 | 1000 | 0.23000 | TreeMap |
| Johnson_et_al_2002 | 2002 | Vert | Bird | Invert | Invert | y | Parasite | Ecto | both | contact | Bird louse | resident | 25 | 25 | 23 | 25 | 1.32 | 1.42 | 19 | 19 | 1000 | 0.23000 | TreeMap |
| Johnson_et_al_2003 | 2003 | Vert | Bird | Invert | Invert | y | Parasite | Ecto | both | contact | Dove wing lice | resident | 28 | 28 | 15 | 31 | 1.48 | 1.33 | 21 | 1 | 100 | 0.03000 | TreeMap |
| Johnson_et_al_2006 | 2006 | Vert | Bird | Invert | Invert | y | Parasite | Ecto | both | contact | Flamingo lice | resident | 10 | 10 | NA | 11 | 1.00 | 1.00 | 11 | 11 | 1000 | 0.40200 | TreeMap |
| Jousselin_et_al_2008 | 2009 | Plant | Plant | Invert | Invert | y | Mutualist | Endo | horizontal | autonomous | Fig wasp | resident | 15 | 15 | 1 | 15 | 1.07 | 1.07 | 14 | 6 | 10000 | 0.01000 | TreeMap |
| Jousselin_et_al_2008 | 2009 | Plant | Plant | Invert | Invert | y | Parasite | Endo | horizontal | autonomous | Fig wasp | resident | 13 | 13 | 1 | 14 | 1.00 | 1.00 | 14 | 1 | 10000 | 0.01000 | TreeMap |
| Jousselin_et_al_2008 | 2009 | Plant | Plant | Invert | Invert | y | Parasite | Endo | horizontal | autonomous | Fig wasp | resident | 13 | 13 | 1 | 13 | 1.00 | 1.00 | 13 | 1 | 10000 | 0.01000 | TreeMap |
| Jousselin_et_al_2008 | 2009 | Plant | Plant | Invert | Invert | y | Parasite | Endo | horizontal | autonomous | Fig wasp | resident | 16 | 16 | 1 | 18 | 1.06 | 1.06 | 17 | 2 | 10000 | 0.01000 | TreeMap |
| Jousselin_et_al_2009 | 2009 | Invert | Invert | Microbe | Bacterium | n | Mutualist | Endo | vertical | vertical | Buchnera | resident | 55 | 22 | 1 | 22 | 1.00 | 1.00 | 22 | 1 | 10000 | 0.00100 | TreeMap |
| Kawaida_et_al_2013 | 2013 | Invert | Invert | Plant | Plant | y | Mutualist | Endo | vertical | vertical | Green algae | resident | 6 | 6 | 1 | 6 | 1.00 | 1.00 | 6 | 1 | 10000 | 0.00350 | TreeMap |
| Kawakita_et_al_2004 | 2004 | Plant | Plant | Invert | Invert | y | Mutualist | Ecto | horizontal | autonomous | Pollinating moth | visitor | 18 | 18 | 1 | 18 | 1.00 | 1.00 | 18 | 1 | 999 | 0.01900 | TreeMap |
| Kelley_&_Farrell_1998 | 1998 | Plant | Plant | Invert | Invert | y | Parasite | Endo | horizontal | autonomous | Bark beetle | resident | 41 | 41 | 1 | 89 | 6.85 | 1.92 | 13 | 1 | 100 | 0.28000 | TreeMap |
| Kikuchi_et_al_2009 | 2009 | Invert | Invert | Microbe | Bacterium | n | Mutualist | Endo | vertical | vertical | Gut symbiont | resident | 14 | 14 | 5 | 14 | 1.00 | 1.00 | 14 | 1 | 1000 | 0.00100 | TreeMap |
| Lanterbecq_et_al_2010 | 2010 | Invert | Invert | Invert | Invert | y | Parasite | Endo/Ecto | horizontal | contact | Myzostomid worm | resident | 16 | 16 | 12 | 16 | 1.00 | 1.00 | 16 | 5 | 5000 | 0.04000 | TreeMap |
| Light_&_Hafner_2008 | 2008 | Vert | Tetrapod | Invert | Invert | y | Parasite | Ecto | both | contact | Rodent sucking lice | resident | 44 | 21 | 4 | 21 | 1.00 | 1.00 | 21 | 1 | 1000 | 0.00100 | TreeMap |
| LimFong_et_al_2008 | 2008 | Invert | Invert | Microbe | Bacterium | n | Mutualist | Endo | vertical | vertical | Endobugula bacteria | resident | 5 | 5 | 1 | 5 | 1.00 | 1.00 | 5 | 2 | 1000 | 0.11000 | TreeMap |
| Liu_et_al_2013 | 2013 | Invert | Invert | Microbe | Bacterium | n | Mutualist | Endo | vertical | vertical | Buchnera | resident | 37 | 37 | 1 | 37 | 1.00 | 1.00 | 37 | 1 | 1000 | 0.00100 | TreeMap |
| Liu_et_al_2014 | 2014 | Invert | Invert | Microbe | Bacterium | n | Mutualist | Endo | vertical | vertical | Buchnera | resident | 27 | 27 | 3 | 29 | 1.00 | 1.00 | 29 | 1 | 1000 | 0.01000 | TreeMap |
| LopezVaamonde_et_al_2001 | 2001 | Invert | Invert | Invert | Invert | y | Parasite | Endo | horizontal | autonomous | Figwasp | resident | 15 | 15 | 1 | 15 | 1.00 | 1.00 | 15 | 1 | 1000 | 0.00100 | TreeMap |
| LopezVaamonde_et_al_2003 | 2003 | Plant | Plant | Invert | Invert | y | Parasite | Endo | horizontal | autonomous | Leaf mining moth | resident | 33 | 33 | 33 | 77 | 1.00 | 1.00 | 77 | 1 | 1000 | 0.21300 | TreeMap |
| LopezVaamonde_et_al_2005 | 2005 | Invert | Invert | Invert | Invert | y | Parasite | Endo | horizontal | autonomous | Parasitic wasp | resident | 28 | 28 | 1 | 35 | 2.33 | 1.33 | 15 | 1 | 1000 | 0.24800 | TreeMap |
| Martin_et_al_1999 | 1999 | Vert | Tetrapod | Microbe | Virus | n | Parasite | Endo | horizontal | bodily fluid | Retrovirus | resident | 38 | 38 | 38 | 48 | 1.00 | 1.00 | 48 | 1 | 1000 | 0.00100 | TreeMap |
| Martin_et_al_2003 | 2003 | Vert | Bird | Microbe | Virus | n | Parasite | Endo | horizontal | bodily fluid | Retrovirus | resident | 14 | 14 | 14 | 16 | 1.00 | 1.00 | 16 | 1 | 100 | 0.01000 | TreeMap |
| Martin_et_al_2003 | 2003 | Vert | Tetrapod | Microbe | Virus | n | Parasite | Endo | horizontal | bodily fluid | Retrovirus | resident | 9 | 9 | 9 | 9 | 1.00 | 1.00 | 9 | 1 | 100 | 0.05000 | TreeMap |
| Martin_et_al_2003 | 2003 | Vert | Tetrapod | Microbe | Virus | n | Parasite | Endo | horizontal | bodily fluid | Retrovirus | resident | 17 | 17 | 17 | 23 | 1.00 | 1.00 | 23 | 1 | 100 | 0.21000 | TreeMap |
| Mazzon_et_al_2010 | 2010 | Invert | Invert | Microbe | Bacterium | n | Mutualist | Endo | vertical | vertical | Stammerula | resident | 17 | 17 | 10 | 17 | 1.06 | 1.13 | 16 | 3 | 1000 | 0.00100 | TreeMap |
| Morelli_&_Spicer_2007 | 2007 | Vert | Bird | Invert | Invert | y | Parasite | Ecto | both | contact | Bird nasal mite | resident | 6 | 6 | 6 | 6 | 1.00 | 1.00 | 6 | 1 | 10000 | 0.00950 | TreeMap |
| Muniz_et_al_2013 | 2013 | Vert | Tetrapod | Microbe | Virus | n | Parasite | Endo | horizontal | bodily fluid | Retrovirus | resident | 17 | 17 | 11 | 17 | 1.00 | 1.00 | 17 | 1 | 10000 | 0.00001 | TreeMap |
| Musser_et_al_2010 | 2010 | Vert | Mammal | Invert | Invert | y | Parasite | Ecto | both | contact | Squirrel sucking lice | resident | 6 | 6 | 1 | 6 | 1.00 | 1.00 | 6 | 6 | 100 | 0.30000 | TreeMap |
| Pagan_et_al_2010 | 2010 | Plant | Plant | Microbe | Virus | n | Parasite | Endo | horizontal | contact | Tobamovirus | resident | 10 | 10 | 10 | 13 | 1.00 | 1.00 | 13 | 1 | 1000 | 0.24000 | TreeMap |
| Page_1996 | 1996 | Vert | Tetrapod | Invert | Invert | y | Parasite | Ecto | both | contact | Gopher chewing lice | resident | 15 | 15 | 6 | 17 | 1.00 | 1.00 | 17 | 2 | 1000 | 0.00100 | TreeMap |
| Page_et_al_1998 | 1998 | Vert | Bird | Invert | Invert | y | Parasite | Ecto | both | contact | Bird lice | resident | 7 | 7 | 1 | 8 | 1.00 | 1.00 | 8 | 1 | 100 | 0.01000 | TreeMap |
| Page_et_al_2004 | 2004 | Vert | Bird | Invert | Invert | y | Parasite | Ecto | both | contact | Seabird lice | resident | 12 | 12 | 4 | 12 | 1.00 | 1.00 | 12 | 1 | 1000 | 0.00100 | TreeMap |
| Page_et_al_2004 | 2004 | Vert | Bird | Invert | Invert | y | Parasite | Ecto | both | contact | Seabird lice | resident | 11 | 11 | 5 | 13 | 1.00 | 1.00 | 13 | 4 | 100 | 0.25000 | TreeMap |
| Page_et_al_2004 | 2004 | Vert | Bird | Invert | Invert | y | Parasite | Ecto | both | contact | Seabird lice | resident | 13 | 13 | 5 | 14 | 1.00 | 1.00 | 14 | 1 | 100 | 0.46000 | TreeMap |
| Page_et_al_2004 | 2004 | Vert | Bird | Invert | Invert | y | Parasite | Ecto | both | contact | Seabird lice | resident | 9 | 9 | 3 | 9 | 1.00 | 1.00 | 9 | 1 | 100 | 0.36000 | TreeMap |
| Paterson_&_Poulin_1999 | 1999 | Vert | Fish | Invert | Invert | y | Parasite | Ecto | horizontal | autonomous | Parasitic copepod | resident | 8 | 8 | 8 | 12 | 1.20 | 2.20 | 10 | 1 | 100 | 0.01000 | TreeMap |
| Paterson_et_al_2000 | 2000 | Vert | Bird | Invert | Invert | y | Parasite | Ecto | both | contact | Seabird lice | resident | 11 | 11 | 5 | 14 | 1.00 | 1.00 | 14 | 5 | 100 | 0.01000 | TreeMap |
| Percy_et_al_2004 | 2004 | Plant | Plant | Invert | Invert | y | Parasite | Ecto | both | autonomous | Psyllid | resident | 35 | 35 | 8 | 56 | 1.22 | 1.09 | 46 | 4 | 1000 | 0.00500 | TreeMap |
| PerezLosada_et_al_2006 | 2006 | Vert | Tetrapod | Microbe | Virus | n | Parasite | Endo | horizontal | NA | Polyomavirus | resident | 9 | 9 | 9 | 11 | 1.00 | 1.00 | 11 | 1 | 100 | 0.01000 | TreeMap |
| Perlman_et_al_2003 | 2003 | Invert | Invert | Invert | Invert | y | Parasite | Endo | horizontal | autonomous | Nematode | resident | 16 | 16 | 1 | 17 | 1.89 | 1.33 | 9 | 1 | 1000 | 0.14000 | TreeMap |
| Quek_et_al_2004 | 2004 | Plant | Plant | Invert | Invert | y | Mutualist | Ecto | horizontal | autonomous | Ants | resident | 11 | 11 | 1 | 23 | 2.30 | 1.60 | 10 | 1 | 1000 | 0.99900 | TreeMap |
| Ramsden_et_al_2008 | 2008 | Vert | Tetrapod | Microbe | Virus | n | Parasite | Endo | horizontal | contact | Hantavirus | resident | 33 | 33 | 20 | 38 | 1.00 | 1.00 | 38 | 1 | 1000 | 0.99900 | TreeMap |
| Reed_et_al_2007 | 2007 | Vert | Tetrapod | Invert | Invert | y | Parasite | Ecto | horizontal | contact | Anthropoid lice | resident | 4 | 4 | 4 | 6 | 1.20 | 1.00 | 5 | 4 | 1000 | 0.05000 | TreeMap |
| Refregier_et_al_2008 | 2008 | Plant | Plant | Microbe | Fungus | y | Parasite | Endo | horizontal | vector | Anther smut fungi | resident | 18 | 18 | 7 | 20 | 1.25 | 1.25 | 16 | 1 | 3000 | 0.50000 | TreeMap |
| Shoemaker_et_al_2002 | 2002 | Invert | Invert | Microbe | Bacterium | n | Mutualist | Endo | both | NA | Wolbachia | resident | 20 | 20 | 7 | 23 | 1.00 | 1.00 | 23 | 1 | 100 | 0.47000 | TreeMap |
| Simkova_et_al_2013 | 2013 | Vert | Fish | Invert | Invert | y | Parasite | Ecto | horizontal | autonomous | Monogenea | resident | 5 | 5 | 1 | 21 | 1.00 | 1.00 | 21 | 1 | 999 | 0.04500 | TreeMap |
| Six_&_Paine_1999 | 1999 | Microbe | Fungus | Invert | Invert | y | Mutualist | Ecto | horizontal | vector | Mycangial fungi | resident | 6 | 6 | 1 | 6 | 1.00 | 1.00 | 6 | 3 | 1000 | 0.03100 | TreeMap |
| Skerikova_et_al_2001 | 2001 | Vert | Fish | Invert | Invert | y | Parasite | Endo | horizontal | trophic | Cestode | resident | 7 | 7 | 7 | 7 | 1.00 | 1.00 | 7 | 1 | 10000 | 0.40000 | TreeMap |
| Smith_et_al_2008b | 2008 | Vert | Tetrapod | Invert | Invert | y | Parasite | Ecto | both | contact | Rodent lice | resident | 20 | 20 | 3 | 20 | 1.00 | 1.00 | 20 | 14 | 100 | 0.05000 | TreeMap |
| Sorenson_et_al_2004 | 2004 | Vert | Bird | Vert | Bird | y | Parasite | Ecto | horizontal | autonomous | Brood parasitic finch | resident | 33 | 33 | 10 | 34 | 1.62 | 1.43 | 21 | 1 | 100 | 0.15000 | TreeMap |
| Subbotin_et_al_2004 | 2004 | Plant | Plant | Invert | Invert | y | Parasite | Endo | horizontal | autonomous | Nematode | resident | 16 | 16 | 16 | 21 | 1.00 | 1.00 | 21 | 4 | 1000 | 0.00100 | TreeMap |
| Switzer_et_al_2005 | 2005 | Vert | Tetrapod | Microbe | Virus | n | Parasite | Endo | horizontal | bodily fluid | Retrovirus | resident | 46 | 46 | 17 | 51 | 1.00 | 1.00 | 51 | 1 | 10000 | 0.00700 | TreeMap |
| Urban_&_Cryan_2012 | 2012 | Invert | Invert | Microbe | Bacterium | n | Mutualist | Endo | vertical | autonomous | Fulgorid planthopper microbe | resident | 40 | 40 | 38 | 40 | 1.00 | 1.00 | 40 | 1 | 1000 | 0.00100 | TreeMap |
| Urban_&_Cryan_2012 | 2012 | Invert | Invert | Microbe | Bacterium | n | Mutualist | Endo | vertical | autonomous | Fulgorid planthopper microbe | resident | 30 | 30 | 29 | 30 | 1.00 | 1.00 | 30 | 1 | 1000 | 0.00100 | TreeMap |
| Vanhove_et_al_2015 | 2015 | Vert | Fish | Invert | Invert | y | Parasite | Endo | horizontal | autonomous | Monogenea | resident | 19 | 19 | 10 | 28 | 1.00 | 1.00 | 28 | 1 | 10000 | 0.04210 | TreeMap |
| Weckstein_2004 | 2004 | Vert | Bird | Invert | Invert | y | Parasite | Ecto | both | contact | Toucan chewing lice | resident | 11 | 11 | 1 | 11 | 2.20 | 1.80 | 5 | 1 | 10000 | 0.89000 | TreeMap |
| Weiblen_&_Bush_2002 | 2002 | Plant | Plant | Invert | Invert | y | Mutualist | Endo | horizontal | autonomous | Fig wasp | resident | 19 | 19 | 1 | 19 | 1.00 | 1.00 | 19 | 1 | 10000 | 0.01950 | TreeMap |
| Weiblen_&_Bush_2002 | 2002 | Plant | Plant | Invert | Invert | y | Parasite | Endo | horizontal | autonomous | Fig wasp | resident | 12 | 12 | 1 | 18 | 1.00 | 1.00 | 18 | 1 | 10000 | 0.12150 | TreeMap |
| Wu_et_al_2008 | 2008 | Plant | Plant | Microbe | Virus | n | Parasite | Endo | horizontal | vector | Mastrevirus | resident | 8 | 8 | 8 | 10 | 1.00 | 1.00 | 10 | 1 | 100 | 0.01000 | TreeMap |
| Yan_et_al_2011 | 2011 | Vert | Fish | Microbe | Virus | n | Parasite | Endo | horizontal | contact | Lymphocystis | resident | 8 | 8 | 8 | 15 | 1.00 | 1.00 | 15 | 1 | 999 | 0.98900 | TreeMap |
| Riess_et_al_2018 | 2018 | Plant | Fungus | Microbe | Fungus | y | Parasite | Endo | horizontal | autonomous | Root fungus | resident | 11 | 11 | 5 | 11 | 1.00 | 1.00 | 11 | 2 | 9999 | 0.26400 | Parafit |
| Souza_et_al_2018 | 2018 | Vert | Mammal | Microbe | Virus | n | Parasite | Endo | both | bodily fluid | Primate hepadnaviruses | resident | 8 | 8 | 8 | 19 | 1.06 | 1.00 | 18 | 1 | 999 | 0.00500 | Parafit |
| Ramasindrazana_et_al_2017 | 2017 | Vert | Mammal | Invert | Invert | y | Parasite | Ecto | both | contact | Bat flies (Nycteribiidae) | resident | 15 | 15 | 6 | 26 | 2.89 | 1.78 | 9 | 5 | 999 | 0.00100 | Parafit |
| Li_et_al_2017 | 2017 | Plant | Plant | Microbe | Fungus | y | Parasite | Endo | horizontal | vector | Grass fungus (Tranzscheliella) | Resident | 12 | 12 | 9 | 12 | 1.71 | 2.00 | 7 | 1 | 999 | 0.50505 | Parafit |
| Sweet_et_al_2018b | 2018 | Vert | Bird | Invert | Invert | y | Parasite | Ecto | both | contact | body lice (Physconelloides) | resident | 11 | 11 | 4 | 13 | 1.86 | 1.43 | 7 | 1 | 100000 | 0.00500 | Parafit |
| Sweet_&_Johnson_2018 | 2018 | Vert | Bird | Invert | Invert | y | Parasite | Ecto | both | contact | wing lice (Columbicola) | resident | 13 | 13 | 4 | 14 | 2.80 | 1.80 | 5 | 1 | 100000 | 0.00500 | Parafit |
| Arab_et_al_2019 | 2019 | Invert | Invert | Microbe | Bacterium | n | Mutualist | Endo | vertical | vertical | Blattabacterium of cockroaches | resident | 55 | 55 | 52 | 55 | 1.00 | 1.00 | 55 | 1 | 999 | 0.00100 | Parafit |
| Sweet_et_al_2018a | 2018 | Vert | Bird | Invert | Invert | y | Parasite | Ecto | both | contact | Brueelia bird lice | resident | 259 | 259 | 163 | 283 | 1.63 | 1.61 | 174 | 11 | 9999 | 0.00010 | Parafit |
| Hewitt_et_al_2019 | 2019 | Vert | Fish | Invert | Invert | y | Parasite | Ecto | horizontal | autonomous | Unionid mussels | resident | 178 | 178 | 79 | 495 | 7.17 | 3.30 | 69 | 35 | 999 | 0.00100 | Parafit |
| Latinne_et_al_2018 | 2018 | Vert | Mammal | Microbe | Funus | y | Parasite | Endo | horizontal | enviromental | Pneumocystis of rodents | resident | 15 | 15 | 6 | 19 | 3.17 | 2.00 | 6 | 1 | 999 | 0.00900 | Parafit |
| Graca_et_al_2018 | 2018 | Vert | Fish | Invert | Invert | y | Parasite | Endo | horizontal | autonomous | Monogenea | resident | 9 | 9 | 7 | 18 | 1.29 | 1.29 | 14 | 1 | 10000 | 0.00010 | Parafit |
| Sweet_et_al_2017 | 2017 | Vert | Bird | Invert | Invert | y | Parasite | Ecto | both | contact | Phabine bird lice | resident | 12 | 12 | 5 | 15 | 1.15 | 1.23 | 13 | 3 | 999 | 0.06900 | Parafit |
| Zhang_et_al_2017 | 2017 | Invert | Invert | Microbe | Bacterium | n | Mutualist | Endo | vertical | vertical | Nardonella of Weevils | resident | 44 | 44 | 24 | 44 | 1.00 | 1.00 | 44 | 1 | 100000 | 0.00001 | Parafit |
| Megia-palma_et_al_2018 | 2018 | Vert | Reptile | Microbe | Protist | y | Parasite | Endo | horizontal | vector | Lizard Schellackia Apicomplexa | resident | 16 | 16 | 8 | 23 | 1.53 | 1.27 | 15 | 8 | 999 | 0.00400 | Parafit |
| Dona_2018 | 2018 | Vert | Bird | Invert | Invert | y | Parasite | Ecto | both | contact | Trouessartia Feather mite | resident | 14 | 14 | 13 | 15 | 1.00 | 1.00 | 15 | 1 | 100000 | 0.01000 | Parafit |
| Dona_2018 | 2018 | Vert | Bird | Invert | Invert | y | Parasite | Ecto | both | contact | Proctophyllodes Feather mite | resident | 42 | 42 | 29 | 44 | 1.00 | 1.00 | 44 | 1 | 100000 | 0.01000 | Parafit |
| Xu_et_el_2017 | 2017 | Invert | Invert | Microbe | Bacterium | n | Mutualist | Endo | vertical | vertical | Buchner | resident | 20 | 20 | 8 | 20 | 1.00 | 1.00 | 20 | 1 | 999 | 0.00100 | Parafit |
| Chen_et_al_2017 | 2017 | Invert | Invert | Microbe | Bacterium | n | Mutualist | Endo | vertical | vertical | Buchnera | resident | 50 | 50 | 11 | 50 | 1.00 | 1.00 | 50 | 1 | 999 | 0.00100 | Parafit |
| Patra_et_al_2018 | 2018 | Vert | Fish | Invert | Invert | y | Parasite | Endo | horizontal | environmental | Myxozoa | resident | 24 | 24 | 24 | 31 | 1.00 | 1.00 | 31 | 1 | 999 | 0.00100 | Parafit |
| Matthews_et_al_2018 | 2018 | Vert | Bird | Invert | Invert | y | Parasite | Ecto | both | contact | Amerodectes feather mites | resident | 12 | 12 | 6 | 33 | 1.00 | 0.58 | 33 | 1 | 99900 | 0.00400 | Parafit |
| Catanach_et_al_2018 | 2018 | Vert | Bird | Invert | Invert | y | Parasite | Ecto | both | contact | Colpocephalum | resident | 54 | 28 | 5 | 44 | 1.07 | 0.93 | 41 | 30 | 999 | 0.00100 | Parafit |
| Ballinger_et_al_2018 | 2018 | Invert | Invert | Microbe | Bacterium | n | Mutualist | Endo | vertical | vertical | Spiroplasma | resident | 11 | 11 | 1 | 12 | 1.00 | 1.00 | 12 | 1 | 999 | 0.07000 | Parafit |
| Li_et_al_2018 | 2018 | Vert | Vert | Invert | Invert | y | Parasite | Endo | horizontal | trophic | Ascarid worms | resident | 68 | 68 | 34 | 129 | 1.45 | NA | 89 | 89 | 100000 | 0.00100 | Parafit |
| Holzer_et_al_2018 | 2018 | Invert | Invert | Invert | Invert | y | Parasite | Endo | horizontal | environmental | Myxozoa | resident | 23 | 23 | 22 | 39 | 1.00 | 1.00 | 39 | 21 | 1000 | 0.00100 | Parafit |
| Holzer_et_al_2018 | 2018 | Vert | Fish | Invert | Invert | y | Parasite | Endo | horizontal | environmental | Myxozoa FW (OIM) | resident | 69 | 69 | 62 | 101 | 1.00 | 1.00 | 101 | 15 | 1000 | 0.00100 | Parafit |
| Holzer_et_al_2018 | 2018 | Vert | Fish | Invert | Invert | y | Parasite | Endo | horizontal | environmental | Myxozoa (PIM) | resident | 69 | 69 | 58 | 75 | 1.00 | 1.00 | 75 | 21 | 1000 | 0.00100 | Parafit |
| Carneiro_et_al_2018 | 2018 | Vert | Mammal | Microbe | Virus | n | Parasite | Endo | horizontal | bodily fluid | Hepatovirus | resident | 26 | 26 | 21 | 26 | 1.00 | 1.00 | 26 | 1 | 100000 | 0.01000 | Parafit |
| Jesovnik_et_al_2017 | 2017 | Invert | Invert | Microbe | Fungus | y | Mutualist | Ecto | both | environmental | Ant fungus | resident | 32 | 6 | 1 | 6 | 1.00 | 1.00 | 6 | 1 | 999 | 0.02900 | Parafit |
| Singh_et_al_2017 | 2017 | Microbe | Fungus | Plant | Plant | y | Mutualist | Endo | vertical | vertical | Lichen algae | resident | 23 | 17 | 1 | 25 | 1.25 | 1.15 | 20 | 1 | 9999 | 0.00020 | Parafit |
| Endara_et_al_2018 | 2018 | Plant | Plant | Invert | Invert | y | Parasite | Endo | horizontal | autonomous | Sawfly | resident | 44 | 30 | 1 | 45 | 1.18 | 1.03 | 38 | NA | 9999 | 0.01500 | Parafit |
| Endara_et_al_2017 | 2017 | Plant | Plant | Invert | Invert | y | Parasite | Ecto | horizontal | autonomous | Gelechioidea moths | visitor | 18 | 18 | 1 | 29 | 1.00 | 2.17 | 29 | NA | 100 | 0.70000 | Parafit |
| Endara_et_al_2017 | 2017 | Plant | Plant | Invert | Invert | y | Parasite | Ecto | horizontal | autonomous | Riodinidae moths | visitor | 10 | 10 | 1 | 18 | 1.50 | 1.25 | 12 | NA | 100 | 0.90000 | Parafit |
| Endara_et_al_2017 | 2017 | Plant | Plant | Invert | Invert | y | Parasite | Ecto | horizontal | autonomous | Erebidae moths | visitor | 14 | 14 | 1 | 18 | 1.20 | 1.13 | 15 | NA | 100 | 0.74000 | Parafit |
| Lauber_et_al_2017 | 2017 | Vert | Vert | Microbe | Virus | n | Parasite | Endo | horizontal | autonomous | Nackednaviruses and Hepadnaviruses | resident | 30 | 30 | 28 | 30 | 0.88 | 1.00 | 34 | 8 | 10000 | 0.00010 | Parafit |
| Althoff_et_al_2012 | 2012 | Plant | Plant | Invert | Invert | y | Mutualist | Ecto | horizontal | autonomous | Yucca moth | visitor | 24 | 24 | 1 | 40 | 2.00 | 1.35 | 20 | 1 | 1000 | 0.00100 | Parafit |
| Althoff_et_al_2012 | 2012 | Plant | Plant | Invert | Invert | y | Mutualist | Ecto | horizontal | autonomous | Yucca moth | visitor | 24 | 24 | 1 | 38 | 2.24 | 1.53 | 17 | 1 | 1000 | 0.00100 | Parafit |
| Banks_et_al_2006 | 2006 | Vert | Bird | Invert | Invert | y | Parasite | Ecto | both | contact | Penguin chewing lice | resident | 18 | 18 | 6 | 30 | 2.00 | 1.60 | 15 | 2 | 10000 | 0.00100 | Parafit |
| Bayerlova_2009 | 2009 | Vert | Mammal | Microbe | Virus | n | Parasite | Endo | horizontal | contact | Arenavirus | resident | 21 | 21 | 14 | 31 | 1.55 | 1.45 | 20 | 1 | 9999 | 0.00040 | Parafit |
| Bellec_et_al_2014 | 2014 | Plant | Plant | Microbe | Virus | n | Parasite | Endo | horizontal | contact | Prasinovirus | resident | 22 | 22 | 3 | 133 | 2.61 | 1.65 | 51 | 1 | 999 | 0.00100 | Parafit |
| Bruyndonckxx_et_al_2009 | 2009 | Vert | Mammal | Invert | Invert | y | Parasite | Ecto | both | contact | Bat mites | resident | 20 | 20 | 7 | 21 | 1.91 | 2.27 | 11 | 2 | 9999 | 0.00300 | Parafit |
| Caraguel_et_al__2007 | 2007 | Microbe | Amoeba | Microbe | Protist | y | Mutualist | Endo | vertical | vertical | Prokinetoplastid endosymbiont | resident | 6 | 6 | 1 | 6 | 1.00 | 1.00 | 6 | 1 | 9999 | 0.00100 | Parafit |
| Choi_&_Thines_2015 | 2015 | Plant | Plant | Microbe | Fungus | y | Parasite | Endo | horizontal | autonomous | Downy mildew | resident | 63 | 63 | 28 | 63 | 1.00 | 1.00 | 63 | 3 | 999 | 0.00100 | Parafit |
| Conord_et_al_2008 | 2008 | Invert | Invert | Microbe | Bacterium | n | Mutualist | Endo | vertical | vertical | Dryophthoridae endosymbionts | resident | 14 | 14 | 10 | 14 | 1.00 | 1.00 | 14 | 1 | 999 | 0.00900 | Parafit |
| Cornuault_et_al_2012 | 2012 | Vert | Bird | Microbe | Protist | y | Parasite | Endo | horizontal | vector | Leucocytozoon | resident | 8 | 8 | 1 | 23 | 1.28 | 1.17 | 18 | 1 | 9999 | 0.03500 | Parafit |
| Cruaud_et_al_2012 | 2012 | Plant | Plant | Invert | Invert | y | Mutualist | Endo | horizontal | autonomous | Fig wasp | resident | 200 | 200 | 1 | 200 | 1.00 | 1.00 | 200 | 20 | 9999 | 0.01000 | Parafit |
| Cui_et_al_2014 | 2014 | Vert | Bird | Microbe | Virus | n | Parasite | Endo | horizontal | bodily fluid | Hepadnavirus | resident | 46 | 46 | 46 | NA | NA | NA | 61 | NA | 99999 | 0.23300 | Parafit |
| Deng_et_al_2013 | 2013 | Invert | Invert | Invert | Invert | y | Parasite | Endo | horizontal | autonomous | Parasitic wasp | resident | 7 | 7 | 4 | 10 | 1.00 | 1.00 | 10 | 2 | 999 | 0.01602 | Parafit |
| Desdevises_et_al_2002 | 2002 | Vert | Fish | Invert | Invert | y | Parasite | Ecto | horizontal | autonomous | Monogenea | resident | 14 | 14 | 11 | 39 | 2.00 | 1.65 | 20 | 2 | 999 | 0.26000 | Parafit |
| Dhami_et_al_2013 | 2013 | Invert | Invert | Microbe | Bacterium | n | Mutualist | Endo | vertical | vertical | Hoataupuhia symbiont | resident | 42 | 42 | NA | 42 | 1.00 | 1.00 | 42 | 4 | 999 | 0.00100 | Parafit |
| Dowie_et_al_2016 | 2016 | Microbe | Fungus | Plant | Plant | y | Parasite | Endo | horizontal | environmental | Parasitic plant | resident | 4 | 4 | 1 | 9 | 2.25 | 1.50 | 4 | 1 | 9999 | 0.00100 | Parafit |
| Du_Toit_et_al_2013 | 2013 | Vert | Mammal | Invert | Invert | y | Parasite | Ecto | both | contact | Rodent lice | resident | 4 | 4 | 1 | 14 | 1.17 | 1.17 | 12 | 1 | 10000 | 0.88000 | Parafit |
| FerrerParis_et_al_2013 | 2013 | Plant | Plant | Invert | Invert | y | Parasite | Ecto | horizontal | autonomous | Butterflies | visitor | 64 | 64 | NA | 112 | 2.73 | 5.20 | 41 | NA | 999 | 0.15700 | Parafit |
| FraijaFernandez_et_al_2016 | 2016 | Vert | Mammal | Invert | Invert | y | Parasite | Endo | horizontal | trophic | Digenea | resident | 31 | 31 | 24 | 50 | 5.56 | 3.67 | 9 | 6 | 999 | 0.00100 | Parafit |
| Garamszegi_2009 | 2009 | Vert | Mammal | Microbe | Protist | y | Parasite | Endo | horizontal | vector | Primate malaria | resident | 23 | 23 | 23 | 43 | 2.39 | 2.56 | 18 | 1 | 1000 | 0.00100 | Parafit |
| Garcia_&_Hayman_2016 | 2016 | Vert | Vert | Microbe | Protist | y | Parasite | Endo | horizontal | trophic | Cryptosporidium | resident | 22 | 22 | 22 | 36 | 1.33 | 1.96 | 27 | 1 | 999 | 0.01000 | Parafit |
| Gavotte_et_al_2007 | 2007 | Microbe | Bacterium | Microbe | Virus | n | Parasite | Endo | both | NA | Bacteriophage | resident | 33 | 33 | 1 | 51 | 0.93 | 1.00 | 55 | 1 | 10000 | 0.13190 | Parafit |
| Goker_et_al_2011 | 2011 | Microbe | Fungus | Microbe | Virus | n | Parasite | Endo | NA | NA | Mycovirus | resident | 8 | 8 | 8 | 8 | 1.00 | 1.00 | 8 | 1 | 9999 | 0.09780 | Parafit |
| Gomard_et_al_2016 | 2016 | Vert | Mammal | Microbe | Bacterium | n | Parasite | Endo | horizontal | NA | Leptospira | resident | 12 | 12 | 11 | 26 | 1.00 | 1.00 | 26 | 1 | 999 | 0.09000 | Parafit |
| Gottschling_et_al_2011 | 2011 | Vert | Mammal | Microbe | Virus | n | Parasite | Endo | horizontal | contact | Papillomavirus | resident | 43 | 43 | 40 | 76 | 0.97 | 1.00 | 78 | 30 | 9999 | 0.00010 | Parafit |
| Hall_et_al__2016 | 2016 | Invert | Invert | Microbe | Bacterium | n | Mutualist | Endo | vertical | vertical | Carsonella primary endosymbiont | resident | 37 | 37 | 18 | 37 | 1.00 | 1.00 | 37 | 1 | 10000 | 0.00100 | Parafit |
| Hall_et_al__2016 | 2016 | Invert | Invert | Microbe | Bacterium | n | Mutualist | Endo | vertical | vertical | Arsenophonus secondary endosymbiont | resident | 20 | 20 | 9 | 20 | 1.00 | 1.00 | 20 | 1 | 10000 | 0.38700 | Parafit |
| Hammer_et_al_2010 | 2010 | Vert | Bird | Invert | Invert | y | Parasite | Ecto | both | contact | Petrel chewing lice | resident | 23 | 23 | 6 | 23 | 1.10 | 1.00 | 21 | 1 | 999 | 0.00100 | Parafit |
| Hammerlinck_et_al_2016 | 2016 | Invert | Invert | Invert | Invert | y | Parasite | Endo | horizontal | autonomous | Parasitic wasp | resident | 11 | 11 | 2 | 11 | 1.38 | 1.13 | 8 | 2 | 999 | 0.12900 | Parafit |
| Hammerlinck_et_al_2016 | 2016 | Invert | Invert | Invert | Invert | y | Parasite | Endo | horizontal | autonomous | Parasitic wasp | resident | 6 | 6 | 2 | 6 | 1.50 | 1.25 | 4 | 2 | 999 | 0.19500 | Parafit |
| Hammerlinck_et_al_2016 | 2016 | Invert | Invert | Invert | Invert | y | Parasite | Endo | horizontal | autonomous | Parasitic wasp | resident | 7 | 7 | 2 | 7 | 1.00 | 1.00 | 7 | 2 | 999 | 0.04200 | Parafit |
| Hembry_et_al_2013 | 2013 | Plant | Plant | Invert | Invert | y | Mutualist | Ecto | horizontal | autonomous | Pollinating moths | visitor | 37 | 37 | 1 | 35 | 1.00 | 1.00 | 35 | 1 | 999 | 0.01700 | Parafit |
| Herrera__et_al_2016 | 2016 | Microbe | Fungus | Microbe | Fungus | y | Parasite | Endo | horizontal | environmental | Mycoparasite Cosmospora | resident | 13 | 13 | 9 | 13 | 1.00 | 1.00 | 13 | 3 | 999 | 0.00500 | Parafit |
| Hoglund_et_al_2003 | 2003 | Vert | Vert | Invert | Invert | y | Parasite | Endo | horizontal | trophic | Lungworm | resident | 8 | 8 | 8 | 10 | 2.00 | 2.40 | 5 | 1 | 10000 | 0.09800 | Parafit |
| Hughes_et_al_2007 | 2007 | Vert | Bird | Invert | Invert | y | Parasite | Ecto | both | contact | Pelican lice | resident | 18 | 18 | 6 | 18 | 1.06 | 1.00 | 17 | 1 | 999 | 0.00010 | Parafit |
| Huyse_&_Volckaert_2005 | 2005 | Vert | Fish | Invert | Invert | y | Parasite | Ecto | horizontal | autonomous | Monogenea | resident | 8 | 8 | 5 | 22 | 1.29 | 1.29 | 17 | 1 | 999 | 0.09500 | Parafit |
| Irwin_et_al_2012 | 2012 | Vert | Mammal | Microbe | Virus | n | Parasite | Endo | horizontal | contact | Arenavirus | resident | 21 | 21 | 14 | 31 | 1.55 | 1.85 | 20 | NA | 9999 | 0.00040 | Parafit |
| Jenkins_et_al_2012 | 2012 | Vert | Bird | Microbe | Protist | y | Parasite | Endo | horizontal | autonomous | Leucocytozoon | resident | 52 | 52 | 40 | 138 | 1.45 | NA | 95 | 1 | 999 | 0.00100 | Parafit |
| Jousselin_et_al_2008 | 2008 | Plant | Plant | Invert | Invert | y | Mutualist | Endo | horizontal | autonomous | Fig wasp | resident | 15 | 15 | 1 | 15 | 1.07 | 1.07 | 14 | 6 | 9999 | 0.00300 | Parafit |
| Jousselin_et_al_2008 | 2008 | Plant | Plant | Invert | Invert | y | Parasite | Endo | horizontal | autonomous | Fig wasp | resident | 13 | 13 | 1 | 13 | 1.00 | 1.00 | 13 | 1 | 9999 | 0.02000 | Parafit |
| Jousselin_et_al_2008 | 2008 | Plant | Plant | Invert | Invert | y | Parasite | Endo | horizontal | autonomous | Fig wasp | resident | 16 | 16 | 1 | 18 | 1.06 | 1.06 | 17 | 2 | 9999 | 0.00100 | Parafit |
| Jousselin_et_al_2008 | 2008 | Plant | Plant | Invert | Invert | y | Parasite | Endo | horizontal | autonomous | Fig wasp | resident | 13 | 13 | 1 | 14 | 1.00 | 1.00 | 14 | 1 | 9999 | 0.00300 | Parafit |
| Jousselin_et_al_2009 | 2009 | Invert | Invert | Microbe | Bacterium | n | Mutualist | Endo | vertical | vertical | Buchnera | resident | 55 | 22 | 1 | 22 | 1.00 | 1.00 | 22 | 1 | 9999 | 0.00100 | Parafit |
| Kaltenpoth_et_al_2014 | 2014 | Invert | Invert | Microbe | Bacterium | n | Mutualist | Endo | vertical | vertical | Beewolf bacterial symbiont | resident | 39 | 39 | 2 | 41 | 1.00 | 1.00 | 41 | 1 | 1000 | 0.00100 | Parafit |
| Kawakita_&_Kato_2009 | 2009 | Plant | Plant | Invert | Invert | y | Mutualist | Ecto | horizontal | autonomous | Yucca moth | visitor | 10 | 10 | 7 | 10 | 1.00 | 1.00 | 10 | 1 | 100 | 0.39000 | Parafit |
| Kawakita_et_al_2004 | 2004 | Plant | Plant | Invert | Invert | y | Mutualist | Ecto | horizontal | autonomous | Pollinating moth | visitor | 18 | 18 | 1 | 18 | 1.00 | 1.00 | 18 | 1 | 999 | 0.00500 | Parafit |
| Kawazoe_et_al_2008 | 2008 | Invert | Invert | Invert | Invert | y | Mutualist | Ecto | vertical | vertical | Bee mite | resident | 4 | 4 | 1 | 5 | 1.25 | 1.25 | 4 | 1 | 9999 | 0.00010 | Parafit |
| Kolsch_&__Pedersen_2010 | 2010 | Invert | Invert | Microbe | Bacterium | n | Mutualist | Endo | vertical | vertical | Reed beetle bacterial endosymbiont | resident | 41 | 41 | 7 | 41 | 1.00 | 1.00 | 41 | 1 | 9999 | 0.00100 | Parafit |
| Krasnov_&_Shenbrot_2013 | 2013 | Vert | Mammal | Invert | Invert | y | Parasite | Ecto | horizontal | contact | Jerboa fleas | resident | 21 | 21 | 8 | 62 | 3.26 | 4.37 | 19 | 7 | 999 | 0.16000 | Parafit |
| Krumbholz_et_al_2009 | 2009 | Vert | Vert | Microbe | Virus | n | Parasite | Endo | horizontal | NA | Polyomavirus | resident | 13 | 13 | 13 | 18 | 1.00 | 1.00 | 18 | 1 | 999999 | 0.49460 | Parafit |
| Ku_&_Hu_2014 | 2014 | Plant | Plant | Microbe | Bacterium | n | Mutualist | Endo | vertical | vertical | Burkholderia plant symbiont | resident | 11 | 11 | 1 | 11 | 1.00 | 1.00 | 11 | 1 | 9999 | 0.02000 | Parafit |
| Lanterbecq_et_al_2010 | 2010 | Invert | Invert | Invert | Invert | y | Parasite | Endo/Ecto | horizontal | contact | Myzostomid worm | resident | 16 | 16 | 12 | 16 | 1.00 | 1.00 | 16 | 5 | 1000 | 0.01300 | Parafit |
| Lauron_et_al_2015 | 2015 | Vert | Bird | Microbe | Protist | y | Parasite | Endo | horizontal | vector | Avian malaria | resident | 18 | 18 | 8 | 83 | 1.80 | NA | 46 | 1 | 1000 | 0.66000 | Parafit |
| Lei_&_Olival_2014 | 2014 | Vert | Mammal | Microbe | Bacterium | n | Parasite | Endo | horizontal | environmental | New World bat Bartonella | resident | 14 | 14 | 11 | 38 | 1.00 | 1.00 | 38 | 1 | 999 | 0.00100 | Parafit |
| Lei_&_Olival_2014 | 2014 | Vert | Mammal | Microbe | Bacterium | n | Parasite | Endo | horizontal | environmental | New World rodent Bartonella | resident | 4 | 4 | 4 | 20 | 1.00 | 1.00 | 20 | 1 | 999 | 0.00100 | Parafit |
| Lei_&_Olival_2014 | 2014 | Vert | Mammal | Microbe | Bacterium | n | Parasite | Endo | horizontal | environmental | New World bat Leptospira | resident | 14 | 14 | 12 | 19 | 1.00 | 1.00 | 19 | 1 | 999 | 0.85800 | Parafit |
| Lei_&_Olival_2014 | 2014 | Vert | Mammal | Microbe | Bacterium | n | Parasite | Endo | horizontal | environmental | Old World bat Bartonella | resident | 9 | 9 | 8 | 13 | 1.00 | 1.00 | 13 | 1 | 999 | 0.02900 | Parafit |
| Lei_&_Olival_2014 | 2014 | Vert | Mammal | Microbe | Bacterium | n | Parasite | Endo | horizontal | environmental | Old World rodent Bartonella | resident | 35 | 35 | 22 | 119 | 1.09 | 1.17 | 109 | 1 | 999 | 0.00010 | Parafit |
| Lei_&_Olival_2014 | 2014 | Vert | Mammal | Microbe | Bacterium | n | Parasite | Endo | horizontal | environmental | Old World bat Leptospira | resident | 6 | 6 | 5 | 7 | 1.00 | 1.00 | 7 | 1 | 999 | 0.75870 | Parafit |
| LewisRogers_&_Crandall_2009 | 2009 | Vert | Tetrapod | Microbe | Virus | n | Parasite | Endo | horizontal | contact | Picornaviridae | resident | 6 | 6 | NA | 27 | 1.00 | 1.00 | 27 | 11 | 999 | 0.47000 | Parafit |
| Li_et_al_2017 | 2017 | Plant | Plant | Microbe | Fungus | y | Parasite | Endo | horizontal | autonomous | Smut fungi | resident | 12 | 12 | 9 | 12 | 1.71 | 1.57 | 7 | 1 | 999 | 0.50505 | Parafit |
| Light_&_Hafner_2008 | 2008 | Vert | Mammal | Invert | Invert | y | Parasite | Ecto | both | contact | Rodent sucking lice | resident | 44 | 21 | 4 | 21 | 1.00 | 1.00 | 21 | 1 | 999 | 0.00100 | Parafit |
| Liu_et_al_2016 | 2016 | Plant | Plant | Microbe | Fungus | y | Parasite | Endo | NA | environmental | Tree foliar fungi | resident | 13 | 13 | 10 | 44 | 1.57 | 2.71 | 28 | 28 | 9999 | 0.02510 | Parafit |
| Liu_et_al_2016 | 2016 | Plant | Plant | Microbe | Fungus | y | Parasite | Endo | NA | environmental | Subtropical tree soil fungi | resident | 19 | 19 | 16 | 76 | 3.30 | 3.22 | 23 | 23 | 9999 | 0.02030 | Parafit |
| Maneesakorn_et_al_2011 | 2011 | Invert | Invert | Microbe | Bacterium | n | Mutualist | Endo | vertical | vertical | Photorhabdus symbiotic bacteria in nematodes | resident | 12 | 12 | 1 | 12 | 1.00 | 1.00 | 12 | 1 | 999 | 0.00100 | Parafit |
| Martinez_et_al_2011 | 2011 | Invert | Invert | Microbe | Protist | y | Parasite | Endo | horizontal | vector | Avian malaria | resident | 16 | 16 | 1 | 22 | 2.44 | 1.56 | 9 | 1 | 999 | 0.07500 | Parafit |
| Martinez_San_udo_&_Girolami_2009 | 2009 | Invert | Invert | Microbe | Bacterium | n | Mutualist | Endo | vertical | vertical | Tephritid symbiotic bacteria | resident | 19 | 19 | 10 | 19 | 1.12 | 1.18 | 17 | 5 | 999 | 0.00300 | Parafit |
| Mattiucci_&_nascetti_2008 | 2008 | Vert | Mammal | Invert | Invert | y | Parasite | Endo | horizontal | trophic | Nematode | resident | 7 | 7 | 15 | 12 | 1.33 | 1.78 | 9 | 1 | 100 | 0.05000 | Parafit |
| Mazzon_et_al_2010 | 2010 | Invert | Invert | Microbe | Bacterium | n | Mutualist | Endo | vertical | vertical | Stammerula bacterial symbiont | resident | 17 | 17 | 10 | 17 | 1.06 | 1.00 | 16 | 3 | 999 | 0.00700 | Parafit |
| McFrederick_&_Taylor_2013 | 2013 | Invert | Invert | Invert | Invert | y | NA | Ecto | vertical | vertical | Nematode | resident | 7 | 7 | 3 | 7 | 1.00 | 1.00 | 7 | 1 | 10000 | 0.00600 | Parafit |
| McKee_et_al_2016 | 2016 | Vert | Mammal | Microbe | Bacterium | n | Parasite | Endo | horizontal | vector | Bat bartonella bacteria | resident | 66 | 66 | 42 | 184 | 1.06 | 1.09 | 173 | 1 | 10000 | 0.00010 | Parafit |
| McLeish_&_Van_Noort_2012 | 2012 | Plant | Plant | Invert | Invert | y | Mutualist | Endo | horizontal | autonomous | Fig wasp | resident | 26 | 26 | 1 | 65 | 1.00 | 1.00 | 65 | 6 | 9999 | 0.18000 | Parafit |
| Mehdiabadi_et_al_2012 | 2012 | Invert | Invert | Microbe | Fungus | y | Mutualist | Ecto | both | environmental | Ant fungus | resident | 99 | 11 | 1 | 11 | 1.00 | 1.00 | 11 | 1 | 999 | 0.00100 | Parafit |
| Mendlova_et_al_2012 | 2012 | Vert | Fish | Invert | Invert | y | Parasite | Ecto | horizontal | autonomous | Monogenea | resident | 6 | 6 | 5 | 34 | 1.17 | 1.21 | 29 | 2 | 999 | 0.02400 | Parafit |
| Merville_et_al._2013 | 2013 | Invert | Invert | Microbe | Bacterium | n | Mutualist | Endo | vertical | vertical | Curculioniphilus buchneri primary endosymbiont of weevils | resident | 9 | 9 | 1 | 9 | 1.00 | 1.00 | 9 | 1 | 999 | 0.00350 | Parafit |
| Millanes_et_al_2014 | 2014 | Microbe | Fungus | Microbe | Fungus | y | Parasite | Endo | both | environmental | Biatoropsis fungus | resident | 16 | 16 | 2 | 16 | 1.00 | 1.00 | 16 | 1 | 999 | 0.23600 | Parafit |
| Miyaki_et_al_2016 | 2016 | Vert | Fish | Microbe | Bacterium | n | Mutualist | Endo | horizontal | environmental | Giant bacteria Epulopiscium | resident | 8 | 8 | 4 | 54 | 3.18 | 2.24 | 17 | 1 | 999 | 0.00100 | Parafit |
| Mondo_et_al_2012 | 2012 | Microbe | Fungus | Microbe | Bacterium | n | Mutualist | Endo | vertical | vertical | Glomeribacter gigasporarum fungal symbiont | resident | 55 | 5 | 2 | 5 | 1.00 | 1.00 | 5 | 1 | 10000 | 0.00010 | Parafit |
| Nouioui_et_al_2014 | 2014 | Plant | Plant | Microbe | Bacterium | n | Mutualist | Endo | horizontal | vector | Frankia | resident | 9 | 9 | 1 | 20 | 1.00 | 1.00 | 20 | 1 | 9999 | 0.33000 | Parafit |
| Pellissier_et_al_2013 | 2013 | Plant | Plant | Invert | Invert | y | Parasite | Ecto | horizontal | autonomous | Butterflies | visitor | 104 | 104 | NA | NA | NA | NA | 97 | NA | 10000 | 0.00010 | Parafit |
| Perkins_2010 | 2010 | Vert | Fish | Invert | Invert | y | Parasite | Endo | horizontal | autonomous | Monogenea | resident | 61 | 61 | 50 | 75 | 1.00 | 1.00 | 75 | NA | 9999 | 0.92600 | Parafit |
| Peterson_et_al_2010 | 2010 | Plant | Plant | Microbe | Fungus | y | Parasite | Endo | horizontal | environmental | Beech fungus | resident | 11 | 11 | 1 | 25 | 2.08 | 1.58 | 12 | 1 | 9999 | 0.00010 | Parafit |
| Polme_et_al_2014.pdf | 2014 | Plant | Plant | Microbe | Bacterium | n | Mutualist | Endo | horizontal | vector | Frankia | resident | 22 | 22 | 1 | NA | NA | NA | 43 | 1 | 999 | 0.00100 | Parafit |
| Quek_et_al_2004 | 2004 | Plant | Plant | Invert | Invert | y | Mutualist | Ecto | horizontal | autonomous | Ant | resident | 10 | 10 | 1 | 23 | 2.30 | 1.70 | 10 | 1 | 999 | 0.77900 | Parafit |
| Ricklefs_et_al_2004 | 2004 | Vert | Bird | Microbe | Protist | y | Parasite | Endo | horizontal | vector | Avian malaria | resident | 44 | 44 | 1 | 121 | 1.86 | NA | 65 | 2 | 100 | 0.63000 | Parafit |
| Savio_2011 | 2011 | Invert | Invert | Microbe | Bacterium | n | Mutualist | Endo | horizontal | NA | Erwinia dacicola tephritid symbiont | resident | 17 | 17 | 10 | 17 | 1.00 | 1.00 | 17 | 3 | 999 | 0.00700 | Parafit |
| Schardl_et_al_2008 | 2008 | Plant | Plant | Microbe | Fungus | y | Mutualist | Endo | both | NA | Grass endophytic fungi (epichloae) | resident | 25 | 25 | 16 | 25 | 0.96 | 1.00 | 26 | 2 | 1000 | 0.00100 | Parafit |
| Sibbald_et_al_2017 | 2017 | Microbe | Amoeba | Microbe | Protist | y | Mutualist | Endo | horizontal | environmental | Paramoeba | resident | 7 | 7 | 1 | 7 | 1.00 | 1.00 | 7 | 1 | 9999 | 0.00010 | Parafit |
| Simkova_et_al_2013 | 2013 | Vert | Fish | Invert | Invert | y | Parasite | Ecto | horizontal | autonomous | Monogenea | resident | 5 | 5 | 1 | 21 | 1.00 | 1.00 | 21 | 1 | 999 | 0.01300 | Parafit |
| Singh_et_al_2016 | 2016 | Microbe | Fungus | Plant | Plant | y | Mutualist | Endo | horizontal | environmental | Trebouxia algae | resident | 23 | 23 | 1 | 28 | 1.40 | 1.20 | 20 | 1 | 9999 | 0.00020 | Parafit |
| Sontowski_et_al_2015 | 2015 | Invert | Invert | Microbe | Bacterium | n | Mutualist | Endo | vertical | vertical | Wolbachia | resident | 14 | 14 | 4 | 14 | 1.00 | 1.00 | 14 | 1 | 100000 | 0.00300 | Parafit |
| Sorenson_et_al_2004 | 2004 | Vert | Bird | Vert | Bird | y | Parasite | Ecto | horizontal | autonomous | Brood parasitic finches | resident | 33 | 33 | 10 | 34 | 1.62 | 1.43 | 21 | 1 | 1000 | 0.00100 | Parafit |
| Stireman_et_al_2010 | 2010 | Plant | Plant | Invert | Invert | y | Parasite | Endo | horizontal | autonomous | Gall midge | resident | 15 | 15 | 10 | 39 | 1.39 | 1.25 | 28 | 1 | 9999 | 0.00080 | Parafit |
| Sudakaran_et_al_2015 | 2015 | Invert | Invert | Microbe | Bacterium | n | Mutualist | Endo | NA | NA | Gordonibacter | resident | 16 | 16 | 7 | 22 | 1.00 | 1.00 | 22 | 1 | 1000 | 0.97800 | Parafit |
| Sudakaran_et_al_2015 | 2015 | Invert | Invert | Microbe | Bacterium | n | Mutualist | Endo | NA | NA | Coriobacterium glomerans | resident | 14 | 14 | 6 | 26 | 1.00 | 1.00 | 26 | 1 | 1000 | 0.97400 | Parafit |
| Summers_&_Rouse_2014 | 2014 | Invert | Invert | Invert | Invert | y | Parasite | Endo/Ecto | horizontal | autonomous | Myzostomida | resident | 53 | 53 | 36 | 78 | 1.13 | 1.23 | 69 | 10 | 9999 | 0.00050 | Parafit |
| Susoy_&_Herrmann_2014 | 2014 | Invert | Invert | Invert | Invert | y | Mutualist | Ecto | vertical | vertical | Nematode | resident | 35 | 35 | 7 | 37 | 1.42 | 1.31 | 26 | 1 | 9999 | 0.00010 | Parafit |
| Swafford_&_Bond_2010 | 2010 | Invert | Invert | Invert | Invert | y | Parasite | Ecto | horizontal | contact | Millipede mite | resident | 7 | 7 | 1 | 7 | 1.00 | 1.00 | 7 | 1 | 9999 | 0.31900 | Parafit |
| Sweet_et_al_2016 | 2016 | Vert | Bird | Invert | Invert | y | Parasite | Ecto | both | contact | Dove wing lice | resident | 52 | 52 | 25 | 57 | 1.33 | 1.21 | 43 | 1 | 100000 | 0.00001 | Parafit |
| Sweet_et_al_2016 | 2016 | Vert | Bird | Invert | Invert | y | Parasite | Ecto | both | contact | Dove body lice | resident | 52 | 52 | 25 | 58 | 1.18 | 1.14 | 49 | 4 | 100000 | 0.00001 | Parafit |
| Tao_et_al_2013 | 2013 | Vert | Tetrapod | Microbe | Virus | n | Parasite | Endo | horizontal | NA | Polyomavirus | resident | 7 | 7 | 7 | 10 | 1.00 | 1.00 | 10 | 1 | 99999 | 0.17592 | Parafit |
| Toju_et_al_2013 | 2013 | Invert | Invert | Microbe | Bacterium | n | Mutualist | Endo | vertical | vertical | Curculioniphilus | resident | 27 | 27 | 4 | 27 | 1.00 | 1.00 | 27 | 1 | 99999 | 0.00001 | Parafit |
| Urban_&_Cryan_2012 | 2012 | Invert | Invert | Microbe | Bacterium | n | Mutualist | Endo | vertical | vertical | Fulgoroidea associated Betaproteobacteria | resident | 30 | 30 | 29 | 30 | 1.00 | 1.00 | 30 | 1 | 1000 | 0.00100 | Parafit |
| Urban_&_Cryan_2012 | 2012 | Invert | Invert | Microbe | Bacterium | n | Mutualist | Endo | vertical | vertical | Fulgoroidea associated Sulcia | resident | 40 | 40 | 38 | 40 | 1.00 | 1.00 | 40 | 1 | 1000 | 0.00300 | Parafit |
| Viale_et_al_2015 | 2015 | Invert | Invert | Microbe | Bacterium | n | Mutualist | Endo | vertical | vertical | Fruit fly Stammerula | resident | 23 | 23 | 1 | 23 | 1.00 | 1.00 | 23 | 1 | 9999 | 0.00100 | Parafit |
| Won_et_al_2008 | 2008 | Invert | Invert | Microbe | Bacterium | n | Mutualist | Endo | horizontal | contact | Mussel thiotroph symbiont | resident | 15 | 15 | 5 | 15 | 1.00 | 1.00 | 15 | 1 | 100 | 0.37000 | Parafit |
A. authors: The authors of the study and the date (citation form).
B. year: Year of publication of the study.
C. host_tax_broad: Separation of the host group according to broader taxonomic units (e.g. vertebrate, invertebrate, microbe, plant).
D. host_tax_fine*: Separation of the host group according to narrower taxonomic units (e.g. fish, tetrapod, bird, invertebrate, protist, bacterium, plant, fungus).
E. symbiont_tax_broad: Separation of the symbiont group according to broader taxonomic units (e.g. vertebrate, invertebrate, microbe, plant).
F. symbiont_tax_fine*: Separation of the symbiont group according to narrower taxonomic units (e.g. invertebrate, protist, virus, bacterium, fungus, plant, bird).
G. symbiont_euk*: Whether the symbiont is eukaryotic (state =‘yes’), or prokaryotic (state=‘no’).
H. symbiosis: The type of symbiont (e.g. parasite or mutualist). For this we followed the definition used by the authors of the study.
I. endo_or_ecto: Whether the symbiont lives outside the host (i.e. is an ectosymbiont), or inside the host (i.e. is an endosymbiont).
J. mode_of_transmission_broad: Whether the symbiont is transmitted vertically, horizontally, or both. For this, we followed the route of transmission specified by the authors of the study
K. mode_of_transmission_fine*: A finer-scale description of the mode of transmission of the symbiont (e.g. contact, vector, bodily fluid, vertical, trophic).
L. symbiont*: Shorthand description of the type of symbiont.
M. Visiting_symbiont?* Whether the symbiont is resident on the host (resident), or makes visits to the host or hosts (visitor).
N. host_tips_linked: The number of individual host taxa included in the cophylogenetic analysis.
O. host_tips_linked_corrected The same measure as for column N, ‘host_tips_linked’, but reduced to only include one member of each host species. This is included because some authors include multiple individuals of the same host species. Without correction, this artificially increases the apparent number of host species included in the study.
P. host_genera: A count of the number of host genera included in the cophylogenetic analysis
Q. total_host_symbioint_links The total number of links between host and symbiont taxa recorded in a study. If all symbionts were strict specialists, this would equal the number of symbionts included in the study. However, because symbionts are often associated with more than one host, this value is often higher than the total number of symbionts included in the study.
R. host_range_link_ratio: An estimation of symbiont host specificity, calculated by dividing the total number of links between hosts and symbionts (i.e. ‘total_host_symbiont_links’, column Q), by the total number of symbionts included in the study (i.e. ‘symbiont_tips_linked’, column T).
S. host_range_taxonomic_breadth: An alternative estimation of symbiont host specificity, calculated by first summing the number of host taxonomic ranks linked to each symbiont (i.e. single host species = 1, multiple host species in the same genera = 2, multiple host genera = 3, multiple host familes = 4, multiple host orders = 5), and dividing by the total number of symbionts included in the study (i.e. ‘symbiont_tips_linked’, column T)
T. symbiont_tips_linked The number of individual symbiont taxa included in the cophylogenetic analysis.
U. symbiont_genera: A count of the number of symbiont genera included in the cophylogenetic analysis.
V. no_randomizations: The number of phylogenetic randomizations performed during the cophylogenetic analysis.
W. p_value: The p-value reported for the cophylogenetic analysis, representing the likelihood that host and symbtion phylogenies display cospeciation.
X. method: Whether TreeMap or Parafit was used to obtain co-divergence or a p value.
We present the number of sample size for two sepreate methods: TreeMap and Parafit (and combined) for effect sizes, papers and different levels of categorical varaibles (factors).
# selecting out variables, which we used for our analysis
dat <- full_data %>% select(-host_tax_fine, -symbiont_tax_fine, -symbiont_euk, -mode_of_transmission_fine, -symbiont, -`Visiting_symbiont?`)
# making a table of sample sizes for different variables
dat %>% group_by(method) %>%
summarise(
`Effect sizes` = n(),
Papers = n_distinct(authors),
`Vertebrate hosts` = sum(host_tax_broad == "Vert", na.rm = T), # na.rm is important when NA exists
`Invertebrate hosts` = sum(host_tax_broad == "Invert", na.rm = T),
`Plant hosts` = sum(host_tax_broad == "Plant", na.rm = T),
`Microbe hosts` = sum(host_tax_broad == "Microbe", na.rm = T),
`Vertebrate symbionts` = sum(symbiont_tax_broad == "Vert", na.rm = T),
`Invertebrate symbionts` = sum(symbiont_tax_broad == "Invert", na.rm = T),
`Plant symbionts` = sum(symbiont_tax_broad == "Plant", na.rm = T),
`Microbe symbionts` = sum(symbiont_tax_broad == "Microbe", na.rm = T),
`Parastic relationships` = sum(symbiosis == "Parasite", na.rm = T),
`Mutualistic relatioships` = sum(symbiosis == "Mutualist", na.rm = T),
`Ecto-symbionts` = sum(endo_or_ecto == "Ecto", na.rm = T),
`Endo-symbionts` = sum(endo_or_ecto == "Endo", na.rm = T),
`Ecto/endo-symbionts` = sum(endo_or_ecto == "Endo/Ecto", na.rm = T),
`Horizontal transmission` = sum(mode_of_transmission_broad == "horizontal", na.rm = T),
`Vertical transmission` = sum(mode_of_transmission_broad == "vertical", na.rm = T),
`Horizontal/vertical-transmission` = sum(mode_of_transmission_broad == "both", na.rm = T)
) -> n_table1
# transposing the table and creating that table and adding a correct number of the papers for `Combined`
n_authors <- n_distinct(dat$authors) # the total number of papers
n_table2 <-t(n_table1[,-1])
colnames(n_table2) <- n_table1$method
n_table2 %>% as_tibble(rownames = "Number") %>%
mutate(Combined = Parafit + TreeMap, Combined = replace(Combined, 2, n_authors)) %>%
rename("Number of" = "Number", "Parafit (n)" = "Parafit", "TreeMap (n)" = "TreeMap", "Combined (n)" = "Combined") %>%
kable() %>% kable_styling("striped", position = "left") %>%
scroll_box(width = "100%", height = "250px")
| Number of | Parafit (n) | TreeMap (n) | Combined (n) |
|---|---|---|---|
| Effect sizes | 140 | 93 | 233 |
| Papers | 118 | 78 | 180 |
| Vertebrate hosts | 60 | 51 | 111 |
| Invertebrate hosts | 39 | 20 | 59 |
| Plant hosts | 31 | 18 | 49 |
| Microbe hosts | 10 | 4 | 14 |
| Vertebrate symbionts | 2 | 1 | 3 |
| Invertebrate symbionts | 61 | 49 | 110 |
| Plant symbionts | 3 | 1 | 4 |
| Microbe symbionts | 74 | 42 | 116 |
| Parastic relationships | 91 | 70 | 161 |
| Mutualistic relatioships | 48 | 23 | 71 |
| Ecto-symbionts | 41 | 34 | 75 |
| Endo-symbionts | 97 | 58 | 155 |
| Ecto/endo-symbionts | 2 | 1 | 3 |
| Horizontal transmission | 84 | 53 | 137 |
| Vertical transmission | 28 | 15 | 43 |
| Horizontal/vertical-transmission | 23 | 25 | 48 |
#pander(split.cell = 40, split.table = Inf) # not as nice as kable
Note that for the numbers of papers do not add up (TreeMap + Parafit \(\neq\) Combined) becuase 16 papers used both TreeMap and Parafit methods (the term “papers” here is our variable auhtors)
Here we have the number of missing data (cells) for all the varaibles used in the analysis below.
# summaring missingness in our dataset
# funs(sum(is.na(.))) needs to be in funs as is.na has "." = each column
dat %>% summarise_all(~sum(is.na(.))) %>% # map(~sum(is.na(.)) # this is an alterantive way
t() %>% as_tibble(rownames = "Variable") %>%
rename("Number of missing data (n)" = "V1") %>%
#pander(split.cell = 40, split.table = Inf)
kable() %>% kable_styling("striped", position = "left") %>%
scroll_box(width = "60%", height = "250px")
| Variable | Number of missing data (n) |
|---|---|
| authors | 0 |
| year | 0 |
| host_tax_broad | 0 |
| symbiont_tax_broad | 0 |
| symbiosis | 1 |
| endo_or_ecto | 0 |
| mode_of_transmission_broad | 5 |
| host_tips_linked | 0 |
| host_tips_linked_corrected | 0 |
| host_genera | 6 |
| total_host_symbioint_links | 3 |
| host_range_link_ratio | 3 |
| host_range_taxonomic_breadth | 7 |
| symbiont_tips_linked | 0 |
| symbiont_genera | 9 |
| no_randomizations | 0 |
| p_value | 0 |
| method | 0 |
# an alternative method using the mi package
#missing_data_tbl <- missing_data.frame(as.data.frame(data))
#show(missing_data_tbl)
Here, we creatde our effect size (correlation coefficent r and its Fisher’s z transformaiton Zr) from p values and associated sample sizes. We used the sum of host_tips_linked_corrected and symbiont_tips_linked as our sample size (i.e., the number of both host and symbiont species) for each effect size (an indicator of congruence). Also, we creat a column with unique ID for each observation (i.e. an observation level random effect), termed observation, which is required for the rma.mv function in metafor.
dat %<>% # getting sample size & observation level random effect
mutate(., sample_size = host_tips_linked_corrected + symbiont_tips_linked, observation = factor(1:nrow(.)))
# calcuating effect size somehow it did not run by piping with above (not
# recognising the first aurgument)
dat %<>% p_to_Zr(p_value, sample_size)
# TODO some factor reordering required!!!
levels = c("small", "medium", "large")
First, we checked what random effects should be put into the main model to do this we fitted two random effects, authors and observation; the former term was added to account for non-independence of effect sizes orginating from the same papers (i.e., authors).
# 2 random effects & model AIC note that probably only base stuff works
# outside of main chunck so need to create AIC here
ma_test1 <- rma.mv(yi = Zr, V = VZr, random = list(~1 | authors, ~1 | observation),
data = dat)
aic1 <- AIC(ma_test1)
# 1 random effect & model AIC
ma_test2 <- rma.mv(yi = Zr, V = VZr, random = ~1 | authors, data = dat)
aic2 <- AIC(ma_test2)
The model (ma_test1), which included both random factors, had a larger AIC value (39.91) than the model with only one random effect (37.91) . This is becuase observation hardly accounted any variance (< 0.0001) compared to authors (0.0327). Therefore, we only had authors as our random factor in subsquentb analyses.
We ran intercept models (meta-analyses) with 3 different datasets (Parafit, TreeMap and both combined; see the explantion of method above). Also, we note that we used adjustments for test statistics and confidence intervals (test = "t"), which is similar to (but not the same as) those proposed by Kanpp and Hartung (2003); probably this approch is a more conservative approach.
# think about making this into a tibble meta-analysis with Parafit
ma_parafit <- rma.mv(yi = Zr, V = VZr, random = ~1 | authors, test = "t", subset = which(method ==
"TreeMap"), data = dat)
# meta-analysis with TreeMap
ma_treemap <- rma.mv(yi = Zr, V = VZr, random = ~1 | authors, test = "t", subset = which(method ==
"Parafit"), data = dat)
# meta-analysis with all the data combined
ma_all <- rma.mv(yi = Zr, V = VZr, test = "t", random = ~1 | authors, data = dat)
Supplementary Table 1: Overall effects (meta-analytic means), 95% confidence intervals (CIs), variance components (V) and heterogeneity, I2 (I2) from metafor model using the 3 datasets (Parafit, TreeMap and both combined, or All). Note that in these models, I2[total] = I2[authors] (see Nakagawa & Santos 2012; REF - probably Senior as well?), as we only have one random factor.
# getting I2 for the models could use map()
i2_treemap <- I2(ma_treemap)
i2_parafit <- I2(ma_parafit)
i2_all <- I2(ma_all)
# creating a table
tibble(Dataset = c("Parafit", "TreeMap", "All"), `Overall mean (Zr)` = c(ma_parafit$b,
ma_treemap$b, ma_all$b), `Lower CI [0.025]` = c(ma_parafit$ci.lb, ma_treemap$ci.lb,
ma_all$ci.lb), `Upper C [0.975]` = c(ma_parafit$ci.ub, ma_treemap$ci.ub,
ma_all$ci.ub), `V[authors]` = c(ma_parafit$sigma2, ma_treemap$sigma2, ma_all$sigma2),
`I2[total]` = c(i2_parafit[1], i2_treemap[1], i2_all[1])) %>% kable("html",
digits = 3) %>% kable_styling("striped", position = "left")
| Dataset | Overall mean (Zr) | Lower CI [0.025] | Upper C [0.975] | V[authors] | I2[total] |
|---|---|---|---|---|---|
| Parafit | 0.333 | 0.273 | 0.394 | 0.036 | 0.523 |
| TreeMap | 0.350 | 0.308 | 0.392 | 0.028 | 0.600 |
| All | 0.345 | 0.309 | 0.381 | 0.033 | 0.590 |
These models gave all consistant results including heterogeneity. Given these results, we proceeded with only analysing the whole dataset (All) from this on.
# creating a table of results
pred_ma <- get_pred(ma_all)
effect_ma <- get_est(ma_all) %>% left_join(pred_ma)
# creating a forest plot
fig_ma <- ggplot(data = effect_ma, aes(x = tanh(estimate), y = "Overall mean")) +
scale_x_continuous(limits = c(-1, 1), breaks = seq(-1, 1, by = 0.2)) + geom_quasirandom(data = dat,
aes(x = tanh(Zr), y = "Overall mean", size = (1/VZr) + 3), groupOnX = FALSE,
alpha = 0.2) + # precition interval (PI)
geom_errorbarh(aes(xmin = tanh(lowerPR), xmax = tanh(upperPR)), height = 0,
show.legend = F, size = 0.5, alpha = 0.6) + # CI
geom_errorbarh(aes(xmin = tanh(lowerCL), xmax = tanh(upperCL)), height = 0,
show.legend = F, size = 1.2) +
geom_vline(xintercept = 0, linetype = 2, colour = "black", alpha = 0.3) + # creating dots and different size (bee-swarm and bubbles)
geom_point(size = 3, shape = 21, fill = "black") + annotate("text", x = -1,
y = "Overall mean", label = paste("italic(k)==", length(dat$Zr)), parse = TRUE,
hjust = "left", size = 3.5) + labs(x = expression(paste(italic(r), " (correlaton)")),
y = "", size = expression(paste(italic(n), " (# of species)"))) + theme_bw() +
theme(legend.position = c(0, 1), legend.justification = c(0, 1)) + theme(legend.direction = "horizontal") +
# theme(legend.background = element_rect(fill = 'white', colour = 'black'))
# +
theme(legend.background = element_blank()) + theme(axis.text.y = element_text(size = 10,
colour = "black", hjust = 0.5, angle = 90))
# ggsave(plot = fig_ma, filename = 'fig_2a.pdf', height = 2, width = 8)
# ggploty 0 does not work (Error in unique.default(x) : unimplemented type
# 'expression' in 'HashTableSetup')
fig_ma
Figure 2a: The effect XXXXXX
We ran a univaraite meta-regression model for each of following moderators: 1) symbiosis, 2) host_tax_broad, 3) symbiont_tax_broad, 4) host_range_link_ratio, 5) host_range_taxonomic_breadth, 6) mode_of_transmission_broad, and 7) endo_or_ecto. The results from these models are presented in the main text.
In addtion to these, we ran three more univariate models: 1) host_tax_symbiosis (equivalent to the interactoin term between symbiosis and host_tax_symbiosis; symbiosis*host_tax_symbiosis), 2) symbiont_tax_symbiosis (symbiosis*symbiont_tax_broad), 3) host_symbiont_tax (host_tax_symbiosis*symbiont_tax_broad) and 4) symbiosis_transmission (symbiosis*mode_of_transmission_broad). There moderators are created below:
dat %<>%
# host_tax_broad*symbiosis (host_tax_symbiosis)
mutate(host_tax_symbiosis = str_c(host_tax_broad, symbiosis),
host_tax_symbiosis = ifelse(host_tax_symbiosis == "InvertNA", NA, host_tax_symbiosis),
host_tax_symbiosis = factor(host_tax_symbiosis),
# symbiont_tax_broad*symbiosis (symbiont_tax_symbiosis)
symbiont_tax_symbiosis = factor(str_c(symbiont_tax_broad, symbiosis)),
# host_tax_broad*symbiont_tax_broad (host_symbiont_tax)
host_symbiont_tax = factor(str_c(host_tax_broad, symbiont_tax_broad)),
# symbiosis*mode_of_transmission_broad (symbiosis_transmission)
symbiosis_transmission = factor(str_c(symbiosis, mode_of_transmission_broad)))
# meta-regression: mutiple intercepts
mr_symbiosis1 <- rma.mv(yi = Zr, V = VZr, mods = ~symbiosis - 1, test = "t",
random = ~1 | authors, data = dat)
# meta-regression: contrast
mr_symbiosis2 <- rma.mv(yi = Zr, V = VZr, mods = ~symbiosis, test = "t", random = ~1 |
authors, data = dat)
Supplementary Table 2: Regression coefficients (Estimate), 95% confidence intervals (CIs), variance components (V) and variance examplained, R2[marginal] (R2) from the meta-regression with symbiosis.
# getting marginal R2
r2_symbiosis1 <- R2(mr_symbiosis1)
# getting estimates
res_symbiosis1 <- get_est(mr_symbiosis1, mod = "symbiosis")
res_symbiosis2 <- get_est(mr_symbiosis2, mod = "symbiosis")
# creating a table
tibble(`Fixed effect` = c(as.character(res_symbiosis1$name), cont_gen(res_symbiosis1$name)),
Estimate = c(res_symbiosis1$estimate, res_symbiosis2$estimate[2]), `Lower CI [0.025]` = c(res_symbiosis1$lowerCL,
res_symbiosis2$lowerCL[2]), `Upper CI [0.975]` = c(res_symbiosis1$upperCL,
res_symbiosis2$upperCL[2]), `V[authors]` = c(mr_symbiosis1$sigma2, rep(NA,
2)), R2 = c(r2_symbiosis1[1], rep(NA, 2))) %>% kable("html", digits = 3) %>%
kable_styling("striped", position = "left")
| Fixed effect | Estimate | Lower CI [0.025] | Upper CI [0.975] | V[authors] | R2 |
|---|---|---|---|---|---|
| Mutualist | 0.411 | 0.349 | 0.473 | 0.031 | 0.064 |
| Parasite | 0.311 | 0.268 | 0.354 | NA | NA |
| Mutualist-Parasite | -0.100 | -0.174 | -0.026 | NA | NA |
# adding sample size (k) for each category
k_symbiosis <- dat %>% group_by(symbiosis) %>% count()
# getting estimates and predicitons
pred_symbiosis <- get_pred(mr_symbiosis1, mod = "symbiosis")
res_symbiosis1 <- left_join(res_symbiosis1, k_symbiosis, by = c("name" = "symbiosis")) %>% left_join(pred_symbiosis)
#res_symbiosis1
# drawing a funnel plot - fig 2b
fig_symbiosis <- ggplot(data = res_symbiosis1, aes(x = tanh(estimate), y = name)) +
scale_x_continuous(limits=c(-1, 1), breaks = seq(-1, 1, by = 0.2) ) +
geom_quasirandom(data = dat %>% filter(!is.na(symbiosis)),
aes(x= tanh(Zr), y = symbiosis, size = ((1/VZr) + 3), colour = symbiosis), groupOnX = FALSE, alpha=0.2) +
# 95 %precition interval (PI)
geom_errorbarh(aes(xmin = tanh(lowerPR), xmax = tanh(upperPR)), height = 0, show.legend = F, size = 0.5, alpha = 0.6) +
# 95 %CI
geom_errorbarh(aes(xmin = tanh(lowerCL), xmax = tanh(upperCL)), height = 0, show.legend = F, size = 1.2) +
geom_vline(xintercept = 0, linetype = 2, colour = "black", alpha = 0.3) +
# creating dots and different size (bee-swarm and bubbles)
geom_point(aes(fill = name), size = 3, shape = 21) + #
# setting colours
scale_color_manual(values = c("Mutualist" = "#E69F00", "Parasite" = "#56B4E9")) +
scale_fill_manual(values = c("Mutualist" = "#E69F00", "Parasite" = "#56B4E9")) +
annotate('text', x = -1, y = res_symbiosis1$name, label= paste("italic(k)==", res_symbiosis1$n), parse=TRUE, hjust = "left", size=3.5) +
labs(x = expression(paste(italic(r), " (correlaton)")), y = "", size = expression(paste(italic(n), " (# of species)")) ) +
guides(fill = "none", colour = "none") +
theme_bw() +
theme(legend.position= c(0, 1), legend.justification = c(0,1)) +
theme(legend.direction="horizontal") +
#theme(legend.background = element_rect(fill = "white", colour = "black")) +
theme(legend.background = element_blank()) +
theme(axis.text.y = element_text(size = 10, colour ="black", hjust = 0.5, angle = 90))
fig_symbiosis
Figure 2b: The effect XXXXXX
# reordering
dat$host_tax_broad <- factor(dat$host_tax_broad, levels = c("Microbe", "Plant",
"Invert", "Vert"))
# sizes <- factor(sizes, levels = c('small', 'medium', 'large')) sizes > [1]
# small large large small medium > Levels: small medium large
# meta-regression: mutiple intercepts
mr_host_tax_broad1 <- rma.mv(yi = Zr, V = VZr, mods = ~host_tax_broad - 1, test = "t",
random = ~1 | authors, data = dat)
# meta-regression: contrast 1
mr_host_tax_broad2 <- rma.mv(yi = Zr, V = VZr, mods = ~host_tax_broad, test = "t",
random = ~1 | authors, data = dat)
# meta-regression: contrast 2
mr_host_tax_broad3 <- rma.mv(yi = Zr, V = VZr, mods = ~relevel(host_tax_broad,
ref = "Plant"), test = "t", random = ~1 | authors, data = dat)
# meta-regression: contrast 3
mr_host_tax_broad4 <- rma.mv(yi = Zr, V = VZr, mods = ~relevel(host_tax_broad,
ref = "Invert"), test = "t", random = ~1 | authors, data = dat)
Supplementary Table 3: Regression coefficients (Estimate), 95% confidence intervals (CIs), variance components (V) and variance examplained, R2[marginal] (R2) from the meta-regression with host_tax_broad.
# getting marginal R2
r2_host_tax_broad1 <- R2(mr_host_tax_broad1)
# getting estimates
res_host_tax_broad1 <- get_est(mr_host_tax_broad1, mod = "host_tax_broad")
res_host_tax_broad2 <- get_est(mr_host_tax_broad2, mod = "host_tax_broad")
# the name bit does not work if relevel....
res_host_tax_broad3 <- get_est(mr_host_tax_broad3, mod = "host_tax_broad")
res_host_tax_broad4 <- get_est(mr_host_tax_broad4, mod = "host_tax_broad")
# creating a table
tibble(`Fixed effect` = c(as.character(res_host_tax_broad1$name), cont_gen(res_host_tax_broad1$name)),
Estimate = c(res_host_tax_broad1$estimate, res_host_tax_broad2$estimate[-1],
res_host_tax_broad3$estimate[-(1:2)], res_host_tax_broad4$estimate[-(1:3)]),
`Lower CI [0.025]` = c(res_host_tax_broad1$lowerCL, res_host_tax_broad2$lowerCL[-1],
res_host_tax_broad3$lowerCL[-(1:2)], res_host_tax_broad4$lowerCL[-(1:3)]),
`Upper CI [0.975]` = c(res_host_tax_broad1$upperCL, res_host_tax_broad2$upperCL[-1],
res_host_tax_broad3$upperCL[-(1:2)], res_host_tax_broad4$upperCL[-(1:3)]),
`V[authors]` = c(mr_host_tax_broad1$sigma2, rep(NA, 9)), R2 = c(r2_host_tax_broad1[1],
rep(NA, 9))) %>% kable("html", digits = 3) %>% kable_styling("striped",
position = "left") %>% scroll_box(width = "100%", height = "300px")
| Fixed effect | Estimate | Lower CI [0.025] | Upper CI [0.975] | V[authors] | R2 |
|---|---|---|---|---|---|
| Microbe | 0.557 | 0.404 | 0.710 | 0.03 | 0.168 |
| Plant | 0.244 | 0.168 | 0.321 | NA | NA |
| Invert | 0.412 | 0.344 | 0.480 | NA | NA |
| Vert | 0.327 | 0.277 | 0.378 | NA | NA |
| Microbe-Plant | -0.312 | -0.483 | -0.141 | NA | NA |
| Microbe-Invert | -0.144 | -0.312 | 0.023 | NA | NA |
| Microbe-Vert | -0.229 | -0.390 | -0.068 | NA | NA |
| Plant-Invert | 0.168 | 0.065 | 0.270 | NA | NA |
| Plant-Vert | 0.083 | -0.009 | 0.175 | NA | NA |
| Invert-Vert | -0.085 | -0.168 | -0.002 | NA | NA |
# adding sample size (k) for each category
k_host_tax_broad <- dat %>% group_by(host_tax_broad) %>% count()
# getting estimates and predicitons
pred_host_tax_broad <- get_pred(mr_host_tax_broad1, mod = "host_tax_broad")
res_host_tax_broad1 <- left_join(res_host_tax_broad1, k_host_tax_broad, by = c("name" = "host_tax_broad")) %>% left_join(pred_host_tax_broad)
#res_symbiosis1
# drawing a funnel plot - fig 2b
fig_host_tax_broad <- ggplot(data = res_host_tax_broad1, aes(x = tanh(estimate), y = name)) +
scale_x_continuous(limits=c(-1, 1), breaks = seq(-1, 1, by = 0.2) ) +
geom_quasirandom(data = dat %>% filter(!is.na(host_tax_broad)),
aes(x= tanh(Zr), y = host_tax_broad, size = ((1/VZr) + 3), colour = host_tax_broad), groupOnX = FALSE, alpha=0.4) +
# 95 %precition interval (PI)
geom_errorbarh(aes(xmin = tanh(lowerPR), xmax = tanh(upperPR)), height = 0, show.legend = F, size = 0.5, alpha = 0.6) +
# 95 %CI
geom_errorbarh(aes(xmin = tanh(lowerCL), xmax = tanh(upperCL)), height = 0, show.legend = F, size = 1.2) +
geom_vline(xintercept = 0, linetype = 2, colour = "black", alpha = 0.3) +
# creating dots and different size (bee-swarm and bubbles)
geom_point(aes(fill = name), size = 3, shape = 21) + #
# setting colours
scale_color_manual(values = c("Microbe" = "#009E73", "Plant" = "#F0E422", "Invert"= "#0072B2", "Vert" = "#D55E00")) +
scale_fill_manual(values = c("Microbe" = "#009E73", "Plant" = "#F0E422", "Invert"= "#0072B2", "Vert" = "#D55E00")) +
scale_y_discrete(labels = c("Microbe" = "Microbe", "Plant" = "Plant", "Invert"= "Invertebrate", "Vert" = "Vertebrate")) +
annotate('text', x = -1, y = res_host_tax_broad1$name, label= paste("italic(k)==", res_host_tax_broad1$n), parse=TRUE, hjust = "left", size=3.5) +
labs(x = expression(paste(italic(r), " (correlaton)")), y = "", size = expression(paste(italic(n), " (# of species)")) ) +
guides(fill = "none", colour = "none") +
theme_bw() +
theme(legend.position= c(0, 1), legend.justification = c(0,1)) +
theme(legend.direction="horizontal") +
#theme(legend.background = element_rect(fill = "white", colour = "black")) +
theme(legend.background = element_blank()) +
theme(axis.text.y = element_text(size = 10, colour ="black", hjust = 0.5, angle = 90))
fig_host_tax_broad
Figure 2c: The effect XXXXXX
# reordering
dat$symbiont_tax_broad <- factor(dat$symbiont_tax_broad, levels = c("Microbe",
"Plant", "Invert", "Vert"))
# sizes <- factor(sizes, levels = c('small', 'medium', 'large')) sizes > [1]
# small large large small medium > Levels: small medium large
# meta-regression: mutiple intercepts
mr_symbiont_tax_broad1 <- rma.mv(yi = Zr, V = VZr, mods = ~symbiont_tax_broad -
1, test = "t", random = ~1 | authors, data = dat)
# meta-regression: contrast 1
mr_symbiont_tax_broad2 <- rma.mv(yi = Zr, V = VZr, mods = ~symbiont_tax_broad,
test = "t", random = ~1 | authors, data = dat)
# meta-regression: contrast 2
mr_symbiont_tax_broad3 <- rma.mv(yi = Zr, V = VZr, mods = ~relevel(symbiont_tax_broad,
ref = "Plant"), test = "t", random = ~1 | authors, data = dat)
# meta-regression: contrast 3
mr_symbiont_tax_broad4 <- rma.mv(yi = Zr, V = VZr, mods = ~relevel(symbiont_tax_broad,
ref = "Invert"), test = "t", random = ~1 | authors, data = dat)
Supplementary Table 3: Regression coefficients (Estimate), 95% confidence intervals (CIs), variance components (V) and variance examplained, R2[marginal] (R2) from the meta-regression with symbiont_tax_broad.
# getting marginal R2
r2_symbiont_tax_broad1 <- R2(mr_symbiont_tax_broad1)
# getting estimates
res_symbiont_tax_broad1 <- get_est(mr_symbiont_tax_broad1, mod = "symbiont_tax_broad")
res_symbiont_tax_broad2 <- get_est(mr_symbiont_tax_broad2, mod = "symbiont_tax_broad")
res_symbiont_tax_broad3 <- get_est(mr_symbiont_tax_broad3, mod = "symbiont_tax_broad")
res_symbiont_tax_broad4 <- get_est(mr_symbiont_tax_broad4, mod = "symbiont_tax_broad")
# creating a table
tibble(`Fixed effect` = c(as.character(res_symbiont_tax_broad1$name), cont_gen(res_symbiont_tax_broad1$name)),
Estimate = c(res_symbiont_tax_broad1$estimate, res_symbiont_tax_broad2$estimate[-1],
res_symbiont_tax_broad3$estimate[-(1:2)], res_symbiont_tax_broad4$estimate[-(1:3)]),
`Lower CI [0.025]` = c(res_symbiont_tax_broad1$lowerCL, res_symbiont_tax_broad2$lowerCL[-1],
res_symbiont_tax_broad3$lowerCL[-(1:2)], res_symbiont_tax_broad4$lowerCL[-(1:3)]),
`Upper CI [0.975]` = c(res_symbiont_tax_broad1$upperCL, res_symbiont_tax_broad2$upperCL[-1],
res_symbiont_tax_broad3$upperCL[-(1:2)], res_symbiont_tax_broad4$upperCL[-(1:3)]),
`V[authors]` = c(mr_symbiont_tax_broad1$sigma2, rep(NA, 9)), R2 = c(r2_symbiont_tax_broad1[1],
rep(NA, 9))) %>% kable("html", digits = 3) %>% kable_styling("striped",
position = "left") %>% scroll_box(width = "100%", height = "300px")
| Fixed effect | Estimate | Lower CI [0.025] | Upper CI [0.975] | V[authors] | R2 |
|---|---|---|---|---|---|
| Microbe | 0.353 | 0.303 | 0.403 | 0.032 | 0.082 |
| Plant | 0.733 | 0.440 | 1.026 | NA | NA |
| Invert | 0.322 | 0.268 | 0.375 | NA | NA |
| Vert | 0.355 | 0.056 | 0.654 | NA | NA |
| Microbe-Plant | 0.380 | 0.083 | 0.678 | NA | NA |
| Microbe-Invert | -0.031 | -0.104 | 0.042 | NA | NA |
| Microbe-Vert | 0.002 | -0.301 | 0.305 | NA | NA |
| Plant-Invert | -0.411 | -0.709 | -0.113 | NA | NA |
| Plant-Vert | -0.378 | -0.797 | 0.041 | NA | NA |
| Invert-Vert | 0.033 | -0.271 | 0.337 | NA | NA |
# adding sample size (k) for each category
k_symbiont_tax_broad <- dat %>% group_by(symbiont_tax_broad) %>% count()
# getting estimates and predicitons
pred_symbiont_tax_broad <- get_pred(mr_symbiont_tax_broad1, mod = "symbiont_tax_broad")
res_symbiont_tax_broad1 <- left_join(res_symbiont_tax_broad1, k_symbiont_tax_broad, by = c("name" = "symbiont_tax_broad")) %>% left_join(pred_symbiont_tax_broad)
#res_symbiosis1
# drawing a funnel plot - fig 2b
fig_symbiont_tax_broad <- ggplot(data = res_symbiont_tax_broad1, aes(x = tanh(estimate), y = name)) +
scale_x_continuous(limits=c(-1, 1), breaks = seq(-1, 1, by = 0.2) ) +
geom_quasirandom(data = dat %>% filter(!is.na(symbiont_tax_broad)),
aes(x= tanh(Zr), y = symbiont_tax_broad, size = ((1/VZr) + 3), colour = symbiont_tax_broad), groupOnX = FALSE, alpha=0.4) +
# 95 %precition interval (PI)
geom_errorbarh(aes(xmin = tanh(lowerPR), xmax = tanh(upperPR)), height = 0, show.legend = F, size = 0.5, alpha = 0.6) +
# 95 %CI
geom_errorbarh(aes(xmin = tanh(lowerCL), xmax = tanh(upperCL)), height = 0, show.legend = F, size = 1.2) +
geom_vline(xintercept = 0, linetype = 2, colour = "black", alpha = 0.3) +
# creating dots and different size (bee-swarm and bubbles)
geom_point(aes(fill = name), size = 3, shape = 21) + #
# setting colours
scale_color_manual(values = c("Microbe" = "#009E73", "Plant" = "#F0E422", "Invert"= "#0072B2", "Vert" = "#D55E00" )) +
scale_fill_manual(values = c("Microbe" = "#009E73", "Plant" = "#F0E422", "Invert"= "#0072B2", "Vert" = "#D55E00")) +
scale_y_discrete(labels = c("Microbe" = "Microbe", "Plant" = "Plant", "Invert"= "Invertebrate", "Vert" = "Vertebrate")) +
annotate('text', x = -1, y = res_symbiont_tax_broad1$name, label= paste("italic(k)==", res_symbiont_tax_broad1$n), parse=TRUE, hjust = "left", size=3.5) +
labs(x = expression(paste(italic(r), " (correlaton)")), y = "", size = expression(paste(italic(n), " (# of species)")) ) +
guides(fill = "none", colour = "none") +
theme_bw() +
theme(legend.position= c(0, 1), legend.justification = c(0,1)) +
theme(legend.direction="horizontal") +
#theme(legend.background = element_rect(fill = "white", colour = "black")) +
theme(legend.background = element_blank()) +
theme(axis.text.y = element_text(size = 10, colour ="black", hjust = 0.5, angle = 90))
fig_symbiont_tax_broad
Figure 2d: The effect XXXXXX
# meta-regression
mr_host_range_link_ratio <- rma.mv(yi = Zr, V = VZr, mods = ~log(host_range_link_ratio),
random = ~1 | authors, data = dat)
Supplementary Table 3: Regression coefficients (Estimate), 95% confidence intervals (CIs), variance components (V) and variance examplained, R2[marginal] (R2) from the meta-regression with symbiont_tax_broad.
# getting marginal R2
r2_host_range_link_ratio <- R2(mr_host_range_link_ratio)
# getting estimates: name does not work for slopes
res_host_range_link_ratio <- get_est(mr_host_range_link_ratio, mod = "log(host_range_link_ratio)")
# creating a table
tibble(`Fixed effect` = c("Intercept", "log(host_range_link_ratio)"), Estimate = c(res_host_range_link_ratio$estimate),
`Lower CI [0.025]` = c(res_host_range_link_ratio$lowerCL), `Upper CI [0.975]` = c(res_host_range_link_ratio$upperCL),
`V[authors]` = c(mr_host_range_link_ratio$sigma2, NA), R2 = c(r2_host_range_link_ratio[1],
NA)) %>% kable("html", digits = 3) %>% kable_styling("striped", position = "left")
| Fixed effect | Estimate | Lower CI [0.025] | Upper CI [0.975] | V[authors] | R2 |
|---|---|---|---|---|---|
| Intercept | 0.360 | 0.318 | 0.401 | 0.033 | 0.012 |
| log(host_range_link_ratio) | -0.057 | -0.150 | 0.037 | NA | NA |
# newmods <- seq(-0.3, 2.2, by = 0.1)
# pred_host_range_link_ratio <-predict.rma(mr_host_range_link_ratio, newmods = newmods)
# ribbon_dat <- tibble(newmods = newmods, ymin = pred_host_range_link_ratio$ci.lb, ymax = pred_host_range_link_ratio$ci.ub)
pred_host_range_link_ratio <-predict.rma(mr_host_range_link_ratio)
# plotting
fig_host_range_link_ratio <- dat %>%
filter(!is.na(host_range_link_ratio)) %>% # getting ride of NA values
mutate(ymin = pred_host_range_link_ratio$ci.lb,
ymax = pred_host_range_link_ratio$ci.ub,
ymin2 = pred_host_range_link_ratio$cr.lb,
ymax2 = pred_host_range_link_ratio$cr.ub,
pred = pred_host_range_link_ratio$pred) %>%
ggplot(aes(x = log(host_range_link_ratio), y = Zr, size = (1/VZr) + 3, )) +
geom_point(shape = 21, fill = "grey90") +
#geom_ribbon(aes(ymin = ymin, ymax = ymax), fill = "#0072B2") + # not quite sure why this does not work
geom_smooth(aes(y = ymin2), method = "loess", se = FALSE, lty = "dotted", lwd = 0.25, colour = "#0072B2") +
geom_smooth(aes(y = ymax2), method = "loess", se = FALSE, lty = "dotted", lwd = 0.25, colour = "#0072B2") +
geom_smooth(aes(y = ymin), method = "loess", se = FALSE,lty = "dotted", lwd = 0.25, colour ="#D55E00") +
geom_smooth(aes(y = ymax), method = "loess", se = FALSE, lty ="dotted", lwd = 0.25, colour ="#D55E00") +
geom_smooth(aes(y = pred), method = "loess", se = FALSE, lty ="dashed", lwd = 0.5, colour ="black") +
ylim(-1, 2) + xlim(-0.05, 2) +
#geom_abline(intercept = mr_host_range_link_ratio$beta[[1]], slope = mr_host_range_link_ratio$beta[[2]], alpha = 0.7, linetype = "dashed", size = 0.5) +
labs(x = "ln(range link ratio)", y = expression(paste(italic(Zr), " (effect size)")), size = expression(paste(italic(n), " (# of species)"))) +
guides(fill = "none", colour = "none") +
# themses
theme_bw() +
theme(legend.position= c(1, 1), legend.justification = c(1, 1)) +
theme(legend.direction="horizontal") +
#theme(legend.background = element_rect(fill = "white", colour = "black")) +
theme(legend.background = element_blank()) +
theme(axis.text.y = element_text(size = 10, colour ="black", hjust = 0.5, angle = 90))
fig_host_range_link_ratio
# meta-regression
mr_host_range_taxonomic_breadth <- rma.mv(yi = Zr, V = VZr, mods = ~log(host_range_taxonomic_breadth),
random = ~1 | authors, data = dat)
Supplementary Table 3: Regression coefficients (Estimate), 95% confidence intervals (CIs), variance components (V) and variance examplained, R2[marginal] (R2) from the meta-regression with symbiont_tax_broad.
# getting marginal R2
r2_host_range_taxonomic_breadth <- R2(mr_host_range_taxonomic_breadth)
# getting estimates: name does not work for slopes
res_host_range_taxonomic_breadth <- get_est(mr_host_range_link_ratio, mod = "log(host_range_link_ratio)")
# creating a table
tibble(`Fixed effect` = c("Intercept", "log(host_range_taxonomic_breadth)"),
Estimate = c(res_host_range_taxonomic_breadth$estimate), `Lower CI [0.025]` = c(res_host_range_taxonomic_breadth$lowerCL),
`Upper CI [0.975]` = c(res_host_range_taxonomic_breadth$upperCL), `V[authors]` = c(mr_host_range_taxonomic_breadth$sigma2,
NA), R2 = c(r2_host_range_taxonomic_breadth[1], NA)) %>% kable("html",
digits = 3) %>% kable_styling("striped", position = "left")
| Fixed effect | Estimate | Lower CI [0.025] | Upper CI [0.975] | V[authors] | R2 |
|---|---|---|---|---|---|
| Intercept | 0.360 | 0.318 | 0.401 | 0.032 | 0.008 |
| log(host_range_taxonomic_breadth) | -0.057 | -0.150 | 0.037 | NA | NA |
pred_host_range_taxonomic_breadth <-predict.rma(mr_host_range_taxonomic_breadth)
# plotting
fig_host_range_taxonomic_breadth <- dat %>%
filter(!is.na(host_range_taxonomic_breadth)) %>% # getting ride of NA values
mutate(ymin = pred_host_range_taxonomic_breadth$ci.lb,
ymax = pred_host_range_taxonomic_breadth$ci.ub,
ymin2 = pred_host_range_taxonomic_breadth$cr.lb,
ymax2 = pred_host_range_taxonomic_breadth$cr.ub,
pred = pred_host_range_taxonomic_breadth$pred) %>%
ggplot(aes(x = log(host_range_taxonomic_breadth), y = Zr, size = (1/VZr) + 3, )) +
geom_point(shape = 21, fill = "grey90") +
#geom_ribbon(aes(ymin = ymin, ymax = ymax), fill = "#0072B2") + # not quite sure why this does not work
geom_smooth(aes(y = ymin2), method = "loess", se = FALSE, lty = "dotted", lwd = 0.25, colour = "#0072B2") +
geom_smooth(aes(y = ymax2), method = "loess", se = FALSE, lty = "dotted", lwd = 0.25, colour = "#0072B2") +
geom_smooth(aes(y = ymin), method = "loess", se = FALSE,lty = "dotted", lwd = 0.25, colour ="#D55E00") +
geom_smooth(aes(y = ymax), method = "loess", se = FALSE, lty ="dotted", lwd = 0.25, colour ="#D55E00") +
geom_smooth(aes(y = pred), method = "loess", se = FALSE, lty ="dashed", lwd = 0.5, colour ="black") +
ylim(-1, 2) + xlim(0, 1.5) +
#geom_abline(intercept = mr_host_range_link_ratio$beta[[1]], slope = mr_host_range_link_ratio$beta[[2]], alpha = 0.7, linetype = "dashed", size = 0.5) +
labs(x = "ln(range link ratio)", y = expression(paste(italic(Zr), " (effect size)")), size = expression(paste(italic(n), " (# of species)"))) +
guides(fill = "none", colour = "none") +
# themses
theme_bw() +
theme(legend.position= c(1, 1), legend.justification = c(1, 1)) +
theme(legend.direction="horizontal") +
#theme(legend.background = element_rect(fill = "white", colour = "black")) +
theme(legend.background = element_blank()) +
theme(axis.text.y = element_text(size = 10, colour ="black", hjust = 0.5, angle = 90))
fig_host_range_taxonomic_breadth
# reordering
dat$endo_or_ecto <- factor(dat$endo_or_ecto, levels = c("Endo/Ecto", "Endo",
"Ecto"))
# meta-regression: mutiple intercepts
mr_endo_or_ecto1 <- rma.mv(yi = Zr, V = VZr, mods = ~endo_or_ecto - 1, test = "t",
random = ~1 | authors, data = dat)
# meta-regression: contrast 1
mr_endo_or_ecto2 <- rma.mv(yi = Zr, V = VZr, mods = ~endo_or_ecto, test = "t",
random = ~1 | authors, data = dat)
# meta-regression: contrast 2
mr_endo_or_ecto3 <- rma.mv(yi = Zr, V = VZr, mods = ~relevel(endo_or_ecto, ref = "Endo"),
test = "t", random = ~1 | authors, data = dat)
Supplementary Table 3: Regression coefficients (Estimate), 95% confidence intervals (CIs), variance components (V) and variance examplained, R2[marginal] (R2) from the meta-regression with endo_or_ecto.
# getting marginal R2
r2_endo_or_ecto1 <- R2(mr_endo_or_ecto1)
# getting estimates
res_endo_or_ecto1 <- get_est(mr_endo_or_ecto1, mod = "endo_or_ecto")
res_endo_or_ecto2 <- get_est(mr_endo_or_ecto2, mod = "endo_or_ecto")
res_endo_or_ecto3 <- get_est(mr_endo_or_ecto3, mod = "endo_or_ecto")
# creating a table
tibble(`Fixed effect` = c(as.character(res_endo_or_ecto1$name), cont_gen(res_endo_or_ecto1$name)),
Estimate = c(res_endo_or_ecto1$estimate, res_endo_or_ecto2$estimate[-1],
res_endo_or_ecto3$estimate[-(1:2)]), `Lower CI [0.025]` = c(res_endo_or_ecto1$lowerCL,
res_endo_or_ecto2$lowerCL[-1], res_endo_or_ecto3$lowerCL[-(1:2)]), `Upper CI [0.975]` = c(res_endo_or_ecto1$upperCL,
res_endo_or_ecto2$upperCL[-1], res_endo_or_ecto3$upperCL[-(1:2)]), `V[authors]` = c(mr_endo_or_ecto1$sigma2,
rep(NA, 5)), R2 = c(r2_endo_or_ecto1[1], rep(NA, 5))) %>% kable("html",
digits = 3) %>% kable_styling("striped", position = "left")
| Fixed effect | Estimate | Lower CI [0.025] | Upper CI [0.975] | V[authors] | R2 |
|---|---|---|---|---|---|
| Endo/Ecto | 0.334 | 0.035 | 0.632 | 0.034 | 0.001 |
| Endo | 0.342 | 0.298 | 0.387 | NA | NA |
| Ecto | 0.353 | 0.287 | 0.418 | NA | NA |
| Endo/Ecto-Endo | 0.009 | -0.293 | 0.311 | NA | NA |
| Endo/Ecto-Ecto | 0.019 | -0.287 | 0.325 | NA | NA |
| Endo-Ecto | 0.010 | -0.069 | 0.090 | NA | NA |
# adding sample size (k) for each category
k_endo_or_ecto <- dat %>% group_by(endo_or_ecto) %>% count()
# getting estimates and predicitons
pred_endo_or_ecto <- get_pred(mr_endo_or_ecto1, mod = "endo_or_ecto")
res_endo_or_ecto1 <- left_join(res_endo_or_ecto1, k_endo_or_ecto, by = c("name" = "endo_or_ecto")) %>% left_join(pred_endo_or_ecto)
#res_symbiosis1
# drawing a funnel plot - fig 2b
fig_endo_or_ecto <- ggplot(data = res_endo_or_ecto1, aes(x = tanh(estimate), y = name)) +
scale_x_continuous(limits=c(-1, 1), breaks = seq(-1, 1, by = 0.2) ) +
geom_quasirandom(data = dat %>% filter(!is.na(endo_or_ecto)),
aes(x= tanh(Zr), y = endo_or_ecto, size = ((1/VZr) + 3), colour = endo_or_ecto), groupOnX = FALSE, alpha=0.4) +
# 95 %precition interval (PI)
geom_errorbarh(aes(xmin = tanh(lowerPR), xmax = tanh(upperPR)), height = 0, show.legend = F, size = 0.5, alpha = 0.6) +
# 95 %CI
geom_errorbarh(aes(xmin = tanh(lowerCL), xmax = tanh(upperCL)), height = 0, show.legend = F, size = 1.2) +
geom_vline(xintercept = 0, linetype = 2, colour = "black", alpha = 0.3) +
# creating dots and different size (bee-swarm and bubbles)
geom_point(aes(fill = name), size = 3, shape = 21) + #
# setting colours
scale_color_manual(values = c("Endo/Ecto" = "#0072B2", "Endo" = "#D55E00", "Ecto"= "#CC79A7")) +
scale_fill_manual(values = c("Endo/Ecto" = "#0072B2", "Endo" = "#D55E00", "Ecto"= "#CC79A7")) +
scale_y_discrete(labels = c("Endo/Ecto" = "Both", "Endo" = "Endosymbiosis", "Ecto"= "Ectosymbiosis")) +
annotate('text', x = -1, y = res_endo_or_ecto1$name, label= paste("italic(k)==", res_endo_or_ecto1$n), parse=TRUE, hjust = "left", size=3.5) +
labs(x = expression(paste(italic(r), " (correlaton)")), y = "", size = expression(paste(italic(n), " (# of species)")) ) +
guides(fill = "none", colour = "none") +
theme_bw() +
theme(legend.position= c(0, 1), legend.justification = c(0,1)) +
theme(legend.direction = "horizontal") +
#theme(legend.background = element_rect(fill = "white", colour = "black")) +
theme(legend.background = element_blank()) +
theme(axis.text.y = element_text(size = 10, colour ="black", hjust = 0.5, angle = 90))
fig_endo_or_ecto
Figure 2g: The effect XXXXXX
# meta-regression: mutiple intercepts
mr_mode_of_transmission_broad1 <- rma.mv(yi = Zr, V = VZr, mods = ~mode_of_transmission_broad -
1, test = "t", random = ~1 | authors, data = dat)
# meta-regression: contrast 1
mr_mode_of_transmission_broad2 <- rma.mv(yi = Zr, V = VZr, mods = ~mode_of_transmission_broad,
test = "t", random = ~1 | authors, data = dat)
# meta-regression: contrast 2
mr_mode_of_transmission_broad3 <- rma.mv(yi = Zr, V = VZr, mods = ~relevel(mode_of_transmission_broad,
ref = "vertical"), test = "t", random = ~1 | authors, data = dat)
Supplementary Table 3: Regression coefficients (Estimate), 95% confidence intervals (CIs), variance components (V) and variance examplained, R2[marginal] (R2) from the meta-regression with mode_of_transmission_broad.
# getting marginal R2
r2_mode_of_transmission_broad1 <- R2(mr_mode_of_transmission_broad1)
# getting estimates
res_mode_of_transmission_broad1 <- get_est(mr_mode_of_transmission_broad1, mod = "mode_of_transmission_broad")
res_mode_of_transmission_broad2 <- get_est(mr_mode_of_transmission_broad2, mod = "mode_of_transmission_broad")
res_mode_of_transmission_broad3 <- get_est(mr_mode_of_transmission_broad3, mod = "mode_of_transmission_broad")
# creating a table
tibble(`Fixed effect` = c(as.character(res_mode_of_transmission_broad1$name),
cont_gen(res_mode_of_transmission_broad1$name)), Estimate = c(res_mode_of_transmission_broad1$estimate,
res_mode_of_transmission_broad2$estimate[-1], res_mode_of_transmission_broad3$estimate[-(1:2)]),
`Lower CI [0.025]` = c(res_mode_of_transmission_broad1$lowerCL, res_mode_of_transmission_broad2$lowerCL[-1],
res_mode_of_transmission_broad3$lowerCL[-(1:2)]), `Upper CI [0.975]` = c(res_mode_of_transmission_broad1$upperCL,
res_mode_of_transmission_broad2$upperCL[-1], res_mode_of_transmission_broad3$upperCL[-(1:2)]),
`V[authors]` = c(mr_mode_of_transmission_broad1$sigma2, rep(NA, 5)), R2 = c(r2_mode_of_transmission_broad1[1],
rep(NA, 5))) %>% kable("html", digits = 3) %>% kable_styling("striped",
position = "left")
| Fixed effect | Estimate | Lower CI [0.025] | Upper CI [0.975] | V[authors] | R2 |
|---|---|---|---|---|---|
| both | 0.371 | 0.298 | 0.443 | 0.024 | 0.219 |
| horizontal | 0.285 | 0.242 | 0.328 | NA | NA |
| vertical | 0.496 | 0.421 | 0.570 | NA | NA |
| both-horizontal | -0.085 | -0.170 | -0.001 | NA | NA |
| both-vertical | 0.125 | 0.021 | 0.229 | NA | NA |
| horizontal-vertical | -0.210 | -0.297 | -0.124 | NA | NA |
# adding sample size (k) for each category
k_mode_of_transmission_broad <- dat %>% group_by(mode_of_transmission_broad) %>% count()
# getting estimates and predicitons
pred_mode_of_transmission_broad <- get_pred(mr_mode_of_transmission_broad1, mod = "mode_of_transmission_broad")
res_mode_of_transmission_broad1 <- left_join(res_mode_of_transmission_broad1, k_mode_of_transmission_broad, by = c("name" = "mode_of_transmission_broad")) %>% left_join(pred_mode_of_transmission_broad)
#res_symbiosis1
# drawing a funnel plot - fig 2b
fig_mode_of_transmission_broad <- ggplot(data = res_mode_of_transmission_broad1, aes(x = tanh(estimate), y = name)) +
scale_x_continuous(limits=c(-1, 1), breaks = seq(-1, 1, by = 0.2) ) +
geom_quasirandom(data = dat %>% filter(!is.na(mode_of_transmission_broad)),
aes(x= tanh(Zr), y = mode_of_transmission_broad, size = ((1/VZr) + 3), colour = mode_of_transmission_broad), groupOnX = FALSE, alpha=0.4) +
# 95 %precition interval (PI)
geom_errorbarh(aes(xmin = tanh(lowerPR), xmax = tanh(upperPR)), height = 0, show.legend = F, size = 0.5, alpha = 0.6) +
# 95 %CI
geom_errorbarh(aes(xmin = tanh(lowerCL), xmax = tanh(upperCL)), height = 0, show.legend = F, size = 1.2) +
geom_vline(xintercept = 0, linetype = 2, colour = "black", alpha = 0.3) +
# creating dots and different size (bee-swarm and bubbles)
geom_point(aes(fill = name), size = 3, shape = 21) + #
# setting colours
scale_color_manual(values = c("both" = "#0072B2", "horizontal" = "#D55E00", "vertical"= "#CC79A7")) +
scale_fill_manual(values = c("both" = "#0072B2", "horizontal" = "#D55E00", "vertical"= "#CC79A7")) +
scale_y_discrete(labels = c("both" = "Both", "horizontal" = "Horizontal", "vertical"= "Vertical")) +
annotate('text', x = -1, y = res_mode_of_transmission_broad1$name, label= paste("italic(k)==", res_mode_of_transmission_broad1$n), parse=TRUE, hjust = "left", size=3.5) +
labs(x = expression(paste(italic(r), " (correlaton)")), y = "", size = expression(paste(italic(n), " (# of species)")) ) +
guides(fill = "none", colour = "none") +
theme_bw() +
theme(legend.position= c(0, 1), legend.justification = c(0,1)) +
theme(legend.direction = "horizontal") +
#theme(legend.background = element_rect(fill = "white", colour = "black")) +
theme(legend.background = element_blank()) +
theme(axis.text.y = element_text(size = 10, colour ="black", hjust = 0.5, angle = 90))
fig_mode_of_transmission_broad
Figure 2g: The effect XXXXXX
# reordering
dat$symbiosis_transmission <- factor(dat$symbiosis_transmission, levels = c("Mutualistboth",
"Mutualisthorizontal", "Mutualistvertical", "Parasiteboth", "Parasitehorizontal"),
labels = c("MutualistBoth", "MutualistHorizontal", "MutualistVertical",
"ParasiteBoth", "ParasiteHorizontal"))
# meta-regression: mutiple intercepts
mr_symbiosis_transmission1 <- rma.mv(yi = Zr, V = VZr, mods = ~symbiosis_transmission -
1, test = "t", random = ~1 | authors, data = dat)
# # meta-regression: contrasts x 10 getting the level names out
level_names <- levels(dat$symbiosis_transmission)
# helper function to run metafor meta-regression
run_rma <- function(name) {
rma.mv(yi = Zr, V = VZr, mods = ~relevel(symbiosis_transmission, ref = name),
test = "t", random = ~1 | authors, data = dat)
}
# results of meta-regression including all contrast results; taking the last
# level out ([-length(level_names)])
mr_symbiosis_transmission <- map(level_names[-length(level_names)], run_rma)
Supplementary Table 3: Regression coefficients (Estimate), 95% confidence intervals (CIs), variance components (V) and variance examplained, R2[marginal] (R2) from the meta-regression with host_tax_broad.
# getting marginal R2
r2_symbiosis_transmission1 <- R2(mr_symbiosis_transmission1)
# getting estimates
res_symbiosis_transmission1 <- get_est(mr_symbiosis_transmission1, mod = "symbiosis_transmission")
res_symbiosis_transmission <- map(mr_symbiosis_transmission, ~get_est(.x, mod = "symbiosis_transmission"))
# a list of the numbers to take out unnecessary contrasts
contra_list <- Map(seq, from = 1, to = 1:4)
# you need to flatten twice: first to make it a list and make it a vector
estiamtes <- map2(res_symbiosis_transmission, contra_list, ~.x[-(.y), "estimate"]) %>%
flatten() %>% flatten_dbl()
lowerCLs <- map2(res_symbiosis_transmission, contra_list, ~.x[-(.y), "lowerCL"]) %>%
flatten() %>% flatten_dbl()
upperCLs <- map2(res_symbiosis_transmission, contra_list, ~.x[-(.y), "upperCL"]) %>%
flatten() %>% flatten_dbl()
# creating a table
tibble(`Fixed effect` = c(as.character(res_symbiosis_transmission1$name), cont_gen(res_symbiosis_transmission1$name)),
Estimate = c(res_symbiosis_transmission1$estimate, estiamtes), `Lower CI [0.025]` = c(res_symbiosis_transmission1$lowerCL,
lowerCLs), `Upper CI [0.975]` = c(res_symbiosis_transmission1$upperCL,
lowerCLs), `V[authors]` = c(mr_symbiosis_transmission1$sigma2, rep(NA,
(5 + choose(5, 2)) - 1)), R2 = c(r2_symbiosis_transmission1[1], rep(NA,
(5 + choose(5, 2)) - 1))) %>% kable("html", digits = 3) %>% kable_styling("striped",
position = "left") %>% scroll_box(width = "100%", height = "300px")
| Fixed effect | Estimate | Lower CI [0.025] | Upper CI [0.975] | V[authors] | R2 |
|---|---|---|---|---|---|
| MutualistBoth | 0.453 | 0.224 | 0.682 | 0.024 | 0.213 |
| MutualistHorizontal | 0.290 | 0.189 | 0.391 | NA | NA |
| MutualistVertical | 0.493 | 0.417 | 0.568 | NA | NA |
| ParasiteBoth | 0.362 | 0.285 | 0.439 | NA | NA |
| ParasiteHorizontal | 0.284 | 0.238 | 0.331 | NA | NA |
| MutualistBoth-MutualistHorizontal | -0.163 | -0.413 | -0.413 | NA | NA |
| MutualistBoth-MutualistVertical | 0.040 | -0.201 | -0.201 | NA | NA |
| MutualistBoth-ParasiteBoth | -0.091 | -0.333 | -0.333 | NA | NA |
| MutualistBoth-ParasiteHorizontal | -0.168 | -0.402 | -0.402 | NA | NA |
| MutualistHorizontal-MutualistVertical | 0.202 | 0.076 | 0.076 | NA | NA |
| MutualistHorizontal-ParasiteBoth | 0.071 | -0.056 | -0.056 | NA | NA |
| MutualistHorizontal-ParasiteHorizontal | -0.006 | -0.115 | -0.115 | NA | NA |
| MutualistVertical-ParasiteBoth | -0.131 | -0.239 | -0.239 | NA | NA |
| MutualistVertical-ParasiteHorizontal | -0.208 | -0.297 | -0.297 | NA | NA |
| ParasiteBoth-ParasiteHorizontal | -0.077 | -0.167 | -0.167 | NA | NA |
# colour list
colour_ls <- c("#000000", "#E69F00", "#56B4E9", "#009E73", "#F0E422", "#0072B2", "#D55E00", "#CC79A7", "#00008B", "#8B0A50", "#54FF9F", "#999999")
# adding sample size (k) for each category
k_symbiosis_transmission <- dat %>% group_by(symbiosis_transmission) %>% count()
# getting estimates and predicitons
pred_symbiosis_transmission <- get_pred(mr_symbiosis_transmission1, mod = "symbiosis_transmission")
res_symbiosis_transmission1 <- left_join(res_symbiosis_transmission1, k_symbiosis_transmission, by = c("name" = "symbiosis_transmission")) %>% left_join(pred_symbiosis_transmission)
#res_symbiosis1
# drawing a funnel plot - fig 2b
fig_symbiosis_transmission <- ggplot(data = res_symbiosis_transmission1, aes(x = tanh(estimate), y = name)) +
scale_x_continuous(limits=c(-1, 1), breaks = seq(-1, 1, by = 0.2) ) +
geom_quasirandom(data = dat %>% filter(!is.na(symbiosis_transmission)),
aes(x= tanh(Zr), y = symbiosis_transmission, size = ((1/VZr) + 3), colour = symbiosis_transmission), groupOnX = FALSE, alpha=0.4) +
# 95 %precition interval (PI)
geom_errorbarh(aes(xmin = tanh(lowerPR), xmax = tanh(upperPR)), height = 0, show.legend = F, size = 0.5, alpha = 0.6) +
# 95 %CI
geom_errorbarh(aes(xmin = tanh(lowerCL), xmax = tanh(upperCL)), height = 0, show.legend = F, size = 1.2) +
geom_vline(xintercept = 0, linetype = 2, colour = "black", alpha = 0.3) +
# creating dots and different size (bee-swarm and bubbles)
geom_point(aes(fill = name), size = 3, shape = 21) + #
# setting colours
scale_color_manual(values = c("MutualistBoth"= colour_ls[1], "MutualistHorizontal"= colour_ls[2], "MutualistVertical" = colour_ls[3],"ParasiteBoth"= colour_ls[4], "ParasiteHorizontal" = colour_ls[5])) +
scale_fill_manual(values = c("MutualistBoth"= colour_ls[1], "MutualistHorizontal"= colour_ls[2], "MutualistVertical" = colour_ls[3],"ParasiteBoth"= colour_ls[4], "ParasiteHorizontal" = colour_ls[5])) +
scale_y_discrete(labels = c("MutualistBoth" = "Mutualist-\nBoth", "MutualistHorizontal" = "Mutualist-\nHorizontal","MutualistVertical" = "Mutualist-\nVertical", "ParasiteBoth" = "Parasite-\nBoth", "ParasiteHorizontal" = "Parasite-\nHorizontal")) +
annotate('text', x = -1, y = res_symbiosis_transmission1$name, label= paste("italic(k)==", res_symbiosis_transmission1$n), parse=TRUE, hjust = "left", size=3.5) +
labs(x = expression(paste(italic(r), " (correlaton)")), y = "", size = expression(paste(italic(n), " (# of species)")) ) +
guides(fill = "none", colour = "none") +
theme_bw() +
theme(legend.position= c(0, 1), legend.justification = c(0,1)) +
theme(legend.direction="horizontal") +
#theme(legend.background = element_rect(fill = "white", colour = "black")) +
theme(legend.background = element_blank()) +
theme(axis.text.y = element_text(size = 10, colour ="black", hjust = 0.5, angle = 90))
fig_symbiosis_transmission
NOTE!!! * Do the REF REF REF * Justification of the use of combined datasets…. - done * just do the main one for all three datasets but not others * or we could - provide forest plots of all the three datasets???? (do it later) * heterogeneity - done
# reordering
dat$host_tax_symbiosis <- factor(dat$host_tax_symbiosis, levels = c("MicrobeMutualist",
"MicrobeParasite", "PlantMutualist", "PlantParasite", "InvertMutualist",
"InvertParasite", "VertMutualist", "VertParasite"))
# meta-regression: mutiple intercepts
mr_host_tax_symbiosis1 <- rma.mv(yi = Zr, V = VZr, mods = ~host_tax_symbiosis -
1, test = "t", random = ~1 | authors, data = dat)
# # meta-regression: contrasts x 10 getting the level names out
level_names <- levels(dat$host_tax_symbiosis)
# helper function to run metafor meta-regression
run_rma <- function(name) {
rma.mv(yi = Zr, V = VZr, mods = ~relevel(host_tax_symbiosis, ref = name),
test = "t", random = ~1 | authors, data = dat)
}
# results of meta-regression including all contrast results; taking the last
# level out ([-length(level_names)])
mr_host_tax_symbiosis <- map(level_names[-length(level_names)], run_rma)
Supplementary Table 3: Regression coefficients (Estimate), 95% confidence intervals (CIs), variance components (V) and variance examplained, R2[marginal] (R2) from the meta-regression with host_tax_broad.
# getting marginal R2
r2_host_tax_symbiosis1 <- R2(mr_host_tax_symbiosis1)
# getting estimates
res_host_tax_symbiosis1 <- get_est(mr_host_tax_symbiosis1, mod = "host_tax_symbiosis")
res_host_tax_symbiosis <- map(mr_host_tax_symbiosis, ~get_est(.x, mod = "host_tax_symbiosis"))
# a list of the numbers to take out unnecessary contrasts
contra_list <- Map(seq, from = 1, to = 1:7)
# you need to flatten twice: first to make it a list and make it a vector
estiamtes <- map2(res_host_tax_symbiosis, contra_list, ~.x[-(.y), "estimate"]) %>%
flatten() %>% flatten_dbl()
lowerCLs <- map2(res_host_tax_symbiosis, contra_list, ~.x[-(.y), "lowerCL"]) %>%
flatten() %>% flatten_dbl()
upperCLs <- map2(res_host_tax_symbiosis, contra_list, ~.x[-(.y), "upperCL"]) %>%
flatten() %>% flatten_dbl()
# creating a table
tibble(`Fixed effect` = c(as.character(res_host_tax_symbiosis1$name), cont_gen(res_host_tax_symbiosis1$name)),
Estimate = c(res_host_tax_symbiosis1$estimate, estiamtes), `Lower CI [0.025]` = c(res_host_tax_symbiosis1$lowerCL,
lowerCLs), `Upper CI [0.975]` = c(res_host_tax_symbiosis1$upperCL,
lowerCLs), `V[authors]` = c(mr_host_tax_symbiosis1$sigma2, rep(NA, (8 +
choose(8, 2)) - 1)), R2 = c(r2_host_tax_symbiosis1[1], rep(NA, (8 +
choose(8, 2)) - 1))) %>% kable("html", digits = 3) %>% kable_styling("striped",
position = "left") %>% scroll_box(width = "100%", height = "300px")
| Fixed effect | Estimate | Lower CI [0.025] | Upper CI [0.975] | V[authors] | R2 |
|---|---|---|---|---|---|
| MicrobeMutualist | 0.806 | 0.596 | 1.015 | 0.027 | 0.296 |
| MicrobeParasite | 0.286 | 0.072 | 0.500 | NA | NA |
| PlantMutualist | 0.241 | 0.129 | 0.354 | NA | NA |
| PlantParasite | 0.246 | 0.155 | 0.337 | NA | NA |
| InvertMutualist | 0.424 | 0.348 | 0.500 | NA | NA |
| InvertParasite | 0.348 | 0.210 | 0.486 | NA | NA |
| VertMutualist | 0.674 | 0.143 | 1.206 | NA | NA |
| VertParasite | 0.321 | 0.272 | 0.371 | NA | NA |
| MicrobeMutualist-MicrobeParasite | -0.520 | -0.819 | -0.819 | NA | NA |
| MicrobeMutualist-PlantMutualist | -0.565 | -0.802 | -0.802 | NA | NA |
| MicrobeMutualist-PlantParasite | -0.560 | -0.788 | -0.788 | NA | NA |
| MicrobeMutualist-InvertMutualist | -0.382 | -0.604 | -0.604 | NA | NA |
| MicrobeMutualist-InvertParasite | -0.458 | -0.708 | -0.708 | NA | NA |
| MicrobeMutualist-VertMutualist | -0.131 | -0.703 | -0.703 | NA | NA |
| MicrobeMutualist-VertParasite | -0.484 | -0.699 | -0.699 | NA | NA |
| MicrobeParasite-PlantMutualist | -0.045 | -0.287 | -0.287 | NA | NA |
| MicrobeParasite-PlantParasite | -0.040 | -0.272 | -0.272 | NA | NA |
| MicrobeParasite-InvertMutualist | 0.138 | -0.089 | -0.089 | NA | NA |
| MicrobeParasite-InvertParasite | 0.062 | -0.193 | -0.193 | NA | NA |
| MicrobeParasite-VertMutualist | 0.389 | -0.185 | -0.185 | NA | NA |
| MicrobeParasite-VertParasite | 0.036 | -0.184 | -0.184 | NA | NA |
| PlantMutualist-PlantParasite | 0.005 | -0.131 | -0.131 | NA | NA |
| PlantMutualist-InvertMutualist | 0.183 | 0.047 | 0.047 | NA | NA |
| PlantMutualist-InvertParasite | 0.107 | -0.071 | -0.071 | NA | NA |
| PlantMutualist-VertMutualist | 0.433 | -0.110 | -0.110 | NA | NA |
| PlantMutualist-VertParasite | 0.080 | -0.042 | -0.042 | NA | NA |
| PlantParasite-InvertMutualist | 0.178 | 0.060 | 0.060 | NA | NA |
| PlantParasite-InvertParasite | 0.102 | -0.063 | -0.063 | NA | NA |
| PlantParasite-VertMutualist | 0.428 | -0.111 | -0.111 | NA | NA |
| PlantParasite-VertParasite | 0.075 | -0.028 | -0.028 | NA | NA |
| InvertMutualist-InvertParasite | -0.076 | -0.234 | -0.234 | NA | NA |
| InvertMutualist-VertMutualist | 0.250 | -0.287 | -0.287 | NA | NA |
| InvertMutualist-VertParasite | -0.103 | -0.193 | -0.193 | NA | NA |
| InvertParasite-VertMutualist | 0.326 | -0.223 | -0.223 | NA | NA |
| InvertParasite-VertParasite | -0.027 | -0.170 | -0.170 | NA | NA |
| VertMutualist-VertParasite | -0.353 | -0.887 | -0.887 | NA | NA |
# adding sample size (k) for each category
k_host_tax_symbiosis <- dat %>% group_by(host_tax_symbiosis) %>% count()
# getting estimates and predicitons
pred_host_tax_symbiosis <- get_pred(mr_host_tax_symbiosis1, mod = "host_tax_symbiosis")
res_host_tax_symbiosis1 <- left_join(res_host_tax_symbiosis1, k_host_tax_symbiosis, by = c("name" = "host_tax_symbiosis")) %>% left_join(pred_host_tax_symbiosis)
#res_symbiosis1
# drawing a funnel plot - fig 2b
fig_host_tax_symbiosis <- ggplot(data = res_host_tax_symbiosis1, aes(x = tanh(estimate), y = name)) +
scale_x_continuous(limits=c(-1, 1), breaks = seq(-1, 1, by = 0.2) ) +
geom_quasirandom(data = dat %>% filter(!is.na(host_tax_symbiosis)),
aes(x= tanh(Zr), y = host_tax_symbiosis, size = ((1/VZr) + 3), colour = host_tax_symbiosis), groupOnX = FALSE, alpha=0.4) +
# 95 %precition interval (PI)
geom_errorbarh(aes(xmin = tanh(lowerPR), xmax = tanh(upperPR)), height = 0, show.legend = F, size = 0.5, alpha = 0.6) +
# 95 %CI
geom_errorbarh(aes(xmin = tanh(lowerCL), xmax = tanh(upperCL)), height = 0, show.legend = F, size = 1.2) +
geom_vline(xintercept = 0, linetype = 2, colour = "black", alpha = 0.3) +
# creating dots and different size (bee-swarm and bubbles)
geom_point(aes(fill = name), size = 3, shape = 21) + #
# setting colours
scale_color_manual(values = c("MicrobeMutualist"= colour_ls[1], "MicrobeParasite"= colour_ls[2], "PlantMutualist"= colour_ls[3], "PlantParasite"= colour_ls[4], "InvertMutualist" = colour_ls[5], "InvertParasite"= colour_ls[6], "VertMutualist"= colour_ls[7], "VertParasite"= colour_ls[8] )) +
scale_fill_manual(values = c("MicrobeMutualist"= colour_ls[1], "MicrobeParasite"= colour_ls[2], "PlantMutualist"= colour_ls[3], "PlantParasite"= colour_ls[4], "InvertMutualist" = colour_ls[5], "InvertParasite"= colour_ls[6], "VertMutualist"= colour_ls[7], "VertParasite"= colour_ls[8] )) +
scale_y_discrete(labels = c("MicrobeMutualist"= "Microbe-\nMutualist", "MicrobeParasite"= "Microbe-\nParasite", "PlantMutualist" = "Plant-\nMutualist", "PlantParasite"="Plant-\nParasite", "InvertMutualist" = "Invertebrate-\nMutualist", "InvertParasite"= "Invertebrate-\nParasite", "VertMutualist"= "Vertebrate-\nMutualist", "VertParasite"= "Vertebrate-\nParasite" )) +
annotate('text', x = -1, y = res_host_tax_symbiosis1$name, label= paste("italic(k)==", res_host_tax_symbiosis1$n), parse=TRUE, hjust = "left", size=3.5) +
labs(x = expression(paste(italic(r), " (correlaton)")), y = "", size = expression(paste(italic(n), " (# of species)")) ) +
guides(fill = "none", colour = "none") +
theme_bw() +
theme(legend.position= c(0, 1), legend.justification = c(0,1)) +
theme(legend.direction="horizontal") +
#theme(legend.background = element_rect(fill = "white", colour = "black")) +
theme(legend.background = element_blank()) +
theme(axis.text.y = element_text(size = 10, colour ="black", hjust = 0.5, angle = 90))
fig_host_tax_symbiosis
NOTE - symbiont_tax_symbiosis = 21 combinations
# reordering
dat$symbiont_tax_symbiosis <- factor(dat$symbiont_tax_symbiosis, levels = c("MicrobeMutualist",
"MicrobeParasite", "PlantMutualist", "PlantParasite", "InvertMutualist",
"InvertParasite", "VertParasite"))
# meta-regression: multiple intercepts
mr_symbiont_tax_symbiosis1 <- rma.mv(yi = Zr, V = VZr, mods = ~symbiont_tax_symbiosis -
1, test = "t", random = ~1 | authors, data = dat)
# # meta-regression: contrasts x 10 getting the level names out
level_names <- levels(dat$symbiont_tax_symbiosis)
# helper function to run metafor meta-regression
run_rma <- function(name) {
rma.mv(yi = Zr, V = VZr, mods = ~relevel(symbiont_tax_symbiosis, ref = name),
test = "t", random = ~1 | authors, data = dat)
}
# results of meta-regression including all contrast results; taking the last
# level out ([-length(level_names)])
mr_symbiont_tax_symbiosis <- map(level_names[-length(level_names)], run_rma)
Supplementary Table 3: Regression coefficients (Estimate), 95% confidence intervals (CIs), variance components (V) and variance examplained, R2[marginal] (R2) from the meta-regression with host_tax_broad.
# getting marginal R2
r2_symbiont_tax_symbiosis1 <- R2(mr_symbiont_tax_symbiosis1)
# getting estimates
res_symbiont_tax_symbiosis1 <- get_est(mr_symbiont_tax_symbiosis1, mod = "symbiont_tax_symbiosis")
res_symbiont_tax_symbiosis <- map(mr_symbiont_tax_symbiosis, ~get_est(.x, mod = "symbiont_tax_symbiosis"))
# a list of the numbers to take out unnecessary contrasts
contra_list <- Map(seq, from = 1, to = 1:6)
# you need to flatten twice: first to make it a list and make it a vector
estiamtes <- map2(res_symbiont_tax_symbiosis, contra_list, ~.x[-(.y), "estimate"]) %>%
flatten() %>% flatten_dbl()
lowerCLs <- map2(res_symbiont_tax_symbiosis, contra_list, ~.x[-(.y), "lowerCL"]) %>%
flatten() %>% flatten_dbl()
upperCLs <- map2(res_symbiont_tax_symbiosis, contra_list, ~.x[-(.y), "upperCL"]) %>%
flatten() %>% flatten_dbl()
# creating a table
tibble(`Fixed effect` = c(as.character(res_symbiont_tax_symbiosis1$name), cont_gen(res_symbiont_tax_symbiosis1$name)),
Estimate = c(res_symbiont_tax_symbiosis1$estimate, estiamtes), `Lower CI [0.025]` = c(res_symbiont_tax_symbiosis1$lowerCL,
lowerCLs), `Upper CI [0.975]` = c(res_symbiont_tax_symbiosis1$upperCL,
lowerCLs), `V[authors]` = c(mr_symbiont_tax_symbiosis1$sigma2, rep(NA,
(7 + choose(7, 2)) - 1)), R2 = c(r2_symbiont_tax_symbiosis1[1], rep(NA,
(7 + choose(7, 2)) - 1))) %>% kable("html", digits = 3) %>% kable_styling("striped",
position = "left") %>% scroll_box(width = "100%", height = "300px")
| Fixed effect | Estimate | Lower CI [0.025] | Upper CI [0.975] | V[authors] | R2 |
|---|---|---|---|---|---|
| MicrobeMutualist | 0.437 | 0.365 | 0.509 | 0.029 | 0.263 |
| MicrobeParasite | 0.279 | 0.213 | 0.345 | NA | NA |
| PlantMutualist | 0.651 | 0.349 | 0.953 | NA | NA |
| PlantParasite | 1.499 | 0.555 | 2.442 | NA | NA |
| InvertMutualist | 0.290 | 0.165 | 0.415 | NA | NA |
| InvertParasite | 0.323 | 0.267 | 0.378 | NA | NA |
| VertParasite | 0.354 | 0.064 | 0.645 | NA | NA |
| MicrobeMutualist-MicrobeParasite | -0.158 | -0.256 | -0.256 | NA | NA |
| MicrobeMutualist-PlantMutualist | 0.214 | -0.097 | -0.097 | NA | NA |
| MicrobeMutualist-PlantParasite | 1.062 | 0.115 | 0.115 | NA | NA |
| MicrobeMutualist-InvertMutualist | -0.147 | -0.292 | -0.292 | NA | NA |
| MicrobeMutualist-InvertParasite | -0.114 | -0.205 | -0.205 | NA | NA |
| MicrobeMutualist-VertParasite | -0.083 | -0.382 | -0.382 | NA | NA |
| MicrobeParasite-PlantMutualist | 0.372 | 0.063 | 0.063 | NA | NA |
| MicrobeParasite-PlantParasite | 1.220 | 0.274 | 0.274 | NA | NA |
| MicrobeParasite-InvertMutualist | 0.011 | -0.130 | -0.130 | NA | NA |
| MicrobeParasite-InvertParasite | 0.044 | -0.042 | -0.042 | NA | NA |
| MicrobeParasite-VertParasite | 0.076 | -0.222 | -0.222 | NA | NA |
| PlantMutualist-PlantParasite | 0.848 | -0.143 | -0.143 | NA | NA |
| PlantMutualist-InvertMutualist | -0.361 | -0.688 | -0.688 | NA | NA |
| PlantMutualist-InvertParasite | -0.328 | -0.635 | -0.635 | NA | NA |
| PlantMutualist-VertParasite | -0.296 | -0.716 | -0.716 | NA | NA |
| PlantParasite-InvertMutualist | -1.209 | -2.161 | -2.161 | NA | NA |
| PlantParasite-InvertParasite | -1.176 | -2.121 | -2.121 | NA | NA |
| PlantParasite-VertParasite | -1.144 | -2.132 | -2.132 | NA | NA |
| InvertMutualist-InvertParasite | 0.033 | -0.100 | -0.100 | NA | NA |
| InvertMutualist-VertParasite | 0.065 | -0.252 | -0.252 | NA | NA |
| InvertParasite-VertParasite | 0.032 | -0.264 | -0.264 | NA | NA |
# adding sample size (k) for each category
k_symbiont_tax_symbiosis <- dat %>% group_by(symbiont_tax_symbiosis) %>% count()
# getting estimates and predicitons
pred_symbiont_tax_symbiosis <- get_pred(mr_symbiont_tax_symbiosis1, mod = "symbiont_tax_symbiosis")
res_symbiont_tax_symbiosis1 <- left_join(res_symbiont_tax_symbiosis1, k_symbiont_tax_symbiosis, by = c("name" = "symbiont_tax_symbiosis")) %>% left_join(pred_symbiont_tax_symbiosis)
#res_symbiosis1
# drawing a funnel plot - fig 2b
fig_symbiont_tax_symbiosis <- ggplot(data = res_symbiont_tax_symbiosis1, aes(x = tanh(estimate), y = name)) +
scale_x_continuous(limits=c(-1, 1), breaks = seq(-1, 1, by = 0.2) ) +
geom_quasirandom(data = dat %>% filter(!is.na(symbiont_tax_symbiosis)),
aes(x= tanh(Zr), y = symbiont_tax_symbiosis, size = ((1/VZr) + 3), colour = symbiont_tax_symbiosis), groupOnX = FALSE, alpha=0.4) +
# 95 %precition interval (PI)
geom_errorbarh(aes(xmin = tanh(lowerPR), xmax = tanh(upperPR)), height = 0, show.legend = F, size = 0.5, alpha = 0.6) +
# 95 %CI
geom_errorbarh(aes(xmin = tanh(lowerCL), xmax = tanh(upperCL)), height = 0, show.legend = F, size = 1.2) +
geom_vline(xintercept = 0, linetype = 2, colour = "black", alpha = 0.3) +
# creating dots and different size (bee-swarm and bubbles)
geom_point(aes(fill = name), size = 3, shape = 21) + #
# setting colours
# setting colours
scale_color_manual(values = c("MicrobeMutualist"= colour_ls[1], "MicrobeParasite"= colour_ls[2], "PlantMutualist"= colour_ls[3], "PlantParasite"= colour_ls[4], "InvertMutualist" = colour_ls[5], "InvertParasite"= colour_ls[6], "VertParasite"= colour_ls[8] )) +
scale_fill_manual(values = c("MicrobeMutualist"= colour_ls[1], "MicrobeParasite"= colour_ls[2], "PlantMutualist"= colour_ls[3], "PlantParasite"= colour_ls[4], "InvertMutualist" = colour_ls[5], "InvertParasite"= colour_ls[6], "VertParasite"= colour_ls[8] )) +
scale_y_discrete(labels = c("MicrobeMutualist"= "Microbe-\nMutualist", "MicrobeParasite"= "Microbe-\nParasite", "PlantMutualist" = "Plant-\nMutualist", "PlantParasite"="Plant-\nParasite", "InvertMutualist" = "Invertebrate-\nMutualist", "InvertParasite"= "Invertebrate-\nParasite", "VertParasite"= "Vertebrate-\nParasite" )) +
annotate('text', x = -1, y = res_symbiont_tax_symbiosis1$name, label= paste("italic(k)==", res_symbiont_tax_symbiosis1$n), parse=TRUE, hjust = "left", size=3.5) +
labs(x = expression(paste(italic(r), " (correlaton)")), y = "", size = expression(paste(italic(n), " (# of species)")) ) +
guides(fill = "none", colour = "none") +
theme_bw() +
theme(legend.position= c(0, 1), legend.justification = c(0, 1)) +
theme(legend.direction="horizontal") +
#theme(legend.background = element_rect(fill = "white", colour = "black")) +
theme(legend.background = element_blank()) +
theme(axis.text.y = element_text(size = 10, colour ="black", hjust = 0.5, angle = 90))
fig_symbiont_tax_symbiosis
NOTE – host_symbiont_tax - 11 varaibles and 55 combinations!!!!
# reordering
dat$host_symbiont_tax <- factor(dat$host_symbiont_tax, levels = c("MicrobeInvert",
"MicrobeMicrobe", "MicrobePlant", "PlantInvert", "PlantMicrobe", "InvertInvert",
"InvertMicrobe", "InvertPlant", "VertInvert", "VertMicrobe", "VertVert"))
# meta-regression: multiple intercepts
mr_host_symbiont_tax1 <- rma.mv(yi = Zr, V = VZr, mods = ~host_symbiont_tax -
1, test = "t", random = ~1 | authors, data = dat)
# # meta-regression: contrasts x 10 getting the level names out
level_names <- levels(dat$host_symbiont_tax)
# helper function to run metafor meta-regression
run_rma <- function(name) {
rma.mv(yi = Zr, V = VZr, mods = ~relevel(host_symbiont_tax, ref = name),
test = "t", random = ~1 | authors, data = dat)
}
# results of meta-regression including all contrast results; taking the last
# level out ([-length(level_names)])
mr_host_symbiont_tax <- map(level_names[-length(level_names)], run_rma)
Supplementary Table 3: Regression coefficients (Estimate), 95% confidence intervals (CIs), variance components (V) and variance examplained, R2[marginal] (R2) from the meta-regression with host_tax_broad.
# getting marginal R2
r2_host_symbiont_tax1 <- R2(mr_host_symbiont_tax1)
# getting estimates
res_host_symbiont_tax1 <- get_est(mr_host_symbiont_tax1, mod = "host_symbiont_tax")
res_host_symbiont_tax <- map(mr_host_symbiont_tax, ~get_est(.x, mod = "host_symbiont_tax"))
# a list of the numbers to take out unnecessary contrasts
contra_list <- Map(seq, from = 1, to = 1:10)
# you need to flatten twice: first to make it a list and make it a vector
estiamtes <- map2(res_host_symbiont_tax, contra_list, ~.x[-(.y), "estimate"]) %>%
flatten() %>% flatten_dbl()
lowerCLs <- map2(res_host_symbiont_tax, contra_list, ~.x[-(.y), "lowerCL"]) %>%
flatten() %>% flatten_dbl()
upperCLs <- map2(res_host_symbiont_tax, contra_list, ~.x[-(.y), "upperCL"]) %>%
flatten() %>% flatten_dbl()
# creating a table
tibble(`Fixed effect` = c(as.character(res_host_symbiont_tax1$name), cont_gen(res_host_symbiont_tax1$name)),
Estimate = c(res_host_symbiont_tax1$estimate, estiamtes), `Lower CI [0.025]` = c(res_host_symbiont_tax1$lowerCL,
lowerCLs), `Upper CI [0.975]` = c(res_host_symbiont_tax1$upperCL, lowerCLs),
`V[authors]` = c(mr_host_tax_symbiosis1$sigma2, rep(NA, (11 + choose(11,
2)) - 1)), R2 = c(r2_host_symbiont_tax1[1], rep(NA, (11 + choose(11,
2)) - 1))) %>% kable("html", digits = 3) %>% kable_styling("striped",
position = "left") %>% scroll_box(width = "100%", height = "300px")
| Fixed effect | Estimate | Lower CI [0.025] | Upper CI [0.975] | V[authors] | R2 |
|---|---|---|---|---|---|
| MicrobeInvert | 0.623 | -0.119 | 1.366 | 0.027 | 0.219 |
| MicrobeMicrobe | 0.508 | 0.328 | 0.689 | NA | NA |
| MicrobePlant | 0.696 | 0.379 | 1.012 | NA | NA |
| PlantInvert | 0.216 | 0.119 | 0.312 | NA | NA |
| PlantMicrobe | 0.295 | 0.167 | 0.423 | NA | NA |
| InvertInvert | 0.421 | 0.286 | 0.556 | NA | NA |
| InvertMicrobe | 0.405 | 0.325 | 0.485 | NA | NA |
| InvertPlant | 0.929 | 0.187 | 1.672 | NA | NA |
| VertInvert | 0.353 | 0.284 | 0.421 | NA | NA |
| VertMicrobe | 0.293 | 0.215 | 0.371 | NA | NA |
| VertVert | 0.355 | 0.059 | 0.650 | NA | NA |
| MicrobeInvert-MicrobeMicrobe | -0.115 | -0.879 | -0.879 | NA | NA |
| MicrobeInvert-MicrobePlant | 0.072 | -0.735 | -0.735 | NA | NA |
| MicrobeInvert-PlantInvert | -0.408 | -1.156 | -1.156 | NA | NA |
| MicrobeInvert-PlantMicrobe | -0.328 | -1.082 | -1.082 | NA | NA |
| MicrobeInvert-InvertInvert | -0.202 | -0.957 | -0.957 | NA | NA |
| MicrobeInvert-InvertMicrobe | -0.218 | -0.965 | -0.965 | NA | NA |
| MicrobeInvert-InvertPlant | 0.306 | -0.744 | -0.744 | NA | NA |
| MicrobeInvert-VertInvert | -0.271 | -1.016 | -1.016 | NA | NA |
| MicrobeInvert-VertMicrobe | -0.330 | -1.077 | -1.077 | NA | NA |
| MicrobeInvert-VertVert | -0.269 | -1.068 | -1.068 | NA | NA |
| MicrobeMicrobe-MicrobePlant | 0.187 | -0.177 | -0.177 | NA | NA |
| MicrobeMicrobe-PlantInvert | -0.293 | -0.498 | -0.498 | NA | NA |
| MicrobeMicrobe-PlantMicrobe | -0.213 | -0.435 | -0.435 | NA | NA |
| MicrobeMicrobe-InvertInvert | -0.087 | -0.313 | -0.313 | NA | NA |
| MicrobeMicrobe-InvertMicrobe | -0.103 | -0.301 | -0.301 | NA | NA |
| MicrobeMicrobe-InvertPlant | 0.421 | -0.343 | -0.343 | NA | NA |
| MicrobeMicrobe-VertInvert | -0.156 | -0.349 | -0.349 | NA | NA |
| MicrobeMicrobe-VertMicrobe | -0.215 | -0.412 | -0.412 | NA | NA |
| MicrobeMicrobe-VertVert | -0.154 | -0.500 | -0.500 | NA | NA |
| MicrobePlant-PlantInvert | -0.480 | -0.811 | -0.811 | NA | NA |
| MicrobePlant-PlantMicrobe | -0.401 | -0.742 | -0.742 | NA | NA |
| MicrobePlant-InvertInvert | -0.275 | -0.619 | -0.619 | NA | NA |
| MicrobePlant-InvertMicrobe | -0.290 | -0.617 | -0.617 | NA | NA |
| MicrobePlant-InvertPlant | 0.234 | -0.573 | -0.573 | NA | NA |
| MicrobePlant-VertInvert | -0.343 | -0.667 | -0.667 | NA | NA |
| MicrobePlant-VertMicrobe | -0.403 | -0.728 | -0.728 | NA | NA |
| MicrobePlant-VertVert | -0.341 | -0.774 | -0.774 | NA | NA |
| PlantInvert-PlantMicrobe | 0.080 | -0.081 | -0.081 | NA | NA |
| PlantInvert-InvertInvert | 0.205 | 0.039 | 0.039 | NA | NA |
| PlantInvert-InvertMicrobe | 0.190 | 0.064 | 0.064 | NA | NA |
| PlantInvert-InvertPlant | 0.714 | -0.035 | -0.035 | NA | NA |
| PlantInvert-VertInvert | 0.137 | 0.019 | 0.019 | NA | NA |
| PlantInvert-VertMicrobe | 0.078 | -0.047 | -0.047 | NA | NA |
| PlantInvert-VertVert | 0.139 | -0.172 | -0.172 | NA | NA |
| PlantMicrobe-InvertInvert | 0.126 | -0.060 | -0.060 | NA | NA |
| PlantMicrobe-InvertMicrobe | 0.110 | -0.041 | -0.041 | NA | NA |
| PlantMicrobe-InvertPlant | 0.634 | -0.119 | -0.119 | NA | NA |
| PlantMicrobe-VertInvert | 0.058 | -0.088 | -0.088 | NA | NA |
| PlantMicrobe-VertMicrobe | -0.002 | -0.152 | -0.152 | NA | NA |
| PlantMicrobe-VertVert | 0.060 | -0.262 | -0.262 | NA | NA |
| InvertInvert-InvertMicrobe | -0.015 | -0.172 | -0.172 | NA | NA |
| InvertInvert-InvertPlant | 0.508 | -0.246 | -0.246 | NA | NA |
| InvertInvert-VertInvert | -0.068 | -0.213 | -0.213 | NA | NA |
| InvertInvert-VertMicrobe | -0.128 | -0.284 | -0.284 | NA | NA |
| InvertInvert-VertVert | -0.066 | -0.391 | -0.391 | NA | NA |
| InvertMicrobe-InvertPlant | 0.524 | -0.223 | -0.223 | NA | NA |
| InvertMicrobe-VertInvert | -0.053 | -0.158 | -0.158 | NA | NA |
| InvertMicrobe-VertMicrobe | -0.112 | -0.224 | -0.224 | NA | NA |
| InvertMicrobe-VertVert | -0.051 | -0.357 | -0.357 | NA | NA |
| InvertPlant-VertInvert | -0.577 | -1.322 | -1.322 | NA | NA |
| InvertPlant-VertMicrobe | -0.636 | -1.383 | -1.383 | NA | NA |
| InvertPlant-VertVert | -0.575 | -1.374 | -1.374 | NA | NA |
| VertInvert-VertMicrobe | -0.060 | -0.163 | -0.163 | NA | NA |
| VertInvert-VertVert | 0.002 | -0.301 | -0.301 | NA | NA |
| VertMicrobe-VertVert | 0.061 | -0.244 | -0.244 | NA | NA |
# colour list
#colour_ls <- c("#000000", "#E69F00", "#56B4E9", "#009E73", "#F0E422", "#0072B2", "#D55E00", "#CC79A7", "#00008B", "#8B0A50", "#54FF9F", "#999999")
# adding sample size (k) for each category
k_host_symbiont_tax <- dat %>% group_by(host_symbiont_tax) %>% count()
# getting estimates and predicitons
pred_host_symbiont_tax <- get_pred(mr_host_symbiont_tax1, mod = "host_symbiont_tax")
res_host_symbiont_tax1 <- left_join(res_host_symbiont_tax1, k_host_symbiont_tax, by = c("name" = "host_symbiont_tax")) %>% left_join(pred_host_symbiont_tax)
#res_symbiosis1
# drawing a funnel plot - fig 2b
fig_host_symbiont_tax <- ggplot(data = res_host_symbiont_tax1, aes(x = tanh(estimate), y = name)) +
scale_x_continuous(limits=c(-1, 1), breaks = seq(-1, 1, by = 0.2) ) +
geom_quasirandom(data = dat %>% filter(!is.na(host_symbiont_tax)),
aes(x= tanh(Zr), y = host_symbiont_tax, size = ((1/VZr) + 3), colour = host_symbiont_tax), groupOnX = FALSE, alpha=0.4) +
# 95 %precition interval (PI)
geom_errorbarh(aes(xmin = tanh(lowerPR), xmax = tanh(upperPR)), height = 0, show.legend = F, size = 0.5, alpha = 0.6) +
# 95 %CI
geom_errorbarh(aes(xmin = tanh(lowerCL), xmax = tanh(upperCL)), height = 0, show.legend = F, size = 1.2) +
geom_vline(xintercept = 0, linetype = 2, colour = "black", alpha = 0.3) +
# creating dots and different size (bee-swarm and bubbles)
geom_point(aes(fill = name), size = 3, shape = 21) + #
# setting colours
scale_color_manual(values = c("MicrobeInvert" = colour_ls[1], "MicrobeMicrobe"= colour_ls[2], "MicrobePlant" = colour_ls[3], "PlantInvert" = colour_ls[4],"PlantMicrobe" = colour_ls[5], "InvertInvert" = colour_ls[6], "InvertMicrobe" = colour_ls[7], "InvertPlant" = colour_ls[8],"VertInvert" = colour_ls[9], "VertMicrobe"= colour_ls[10],"VertVert" = colour_ls[11])) +
scale_fill_manual(values = c("MicrobeInvert" = colour_ls[1], "MicrobeMicrobe"= colour_ls[2], "MicrobePlant" = colour_ls[3], "PlantInvert" = colour_ls[4],"PlantMicrobe" = colour_ls[5], "InvertInvert" = colour_ls[6], "InvertMicrobe" = colour_ls[7], "InvertPlant" = colour_ls[8],"VertInvert" = colour_ls[9], "VertMicrobe"= colour_ls[10],"VertVert" = colour_ls[11])) +
scale_y_discrete(labels = c("MicrobeInvert" = "Microbe-\nInvertebrate", "MicrobeMicrobe"= "Microbe-\nMicrobe", "MicrobePlant" = "Microbe-\nPlant", "PlantInvert" = "Plant-\nInvertebrate","PlantMicrobe" = "Plant-\nMicrobe", "InvertInvert" = "Invertebrate\nInvertebrate", "InvertMicrobe" = "Invertebrate-\nMicrobe", "InvertPlant" = "Invertebrate-\nPlant","VertInvert" = "Vertebrate-\nInvertebrate", "VertMicrobe"= "Vertebrate-\nMicrobe", "VertVert" = "Vertebrate-\nVertebrate")) +
annotate('text', x = -1, y = res_host_symbiont_tax1$name, label= paste("italic(k)==", res_host_symbiont_tax1$n), parse=TRUE, hjust = "left", size=3.5) +
labs(x = expression(paste(italic(r), " (correlaton)")), y = "", size = expression(paste(italic(n), " (# of species)")) ) +
guides(fill = "none", colour = "none") +
theme_bw() +
theme(legend.position= c(0, 1), legend.justification = c(0,1)) +
theme(legend.direction="horizontal") +
#theme(legend.background = element_rect(fill = "white", colour = "black")) +
theme(legend.background = element_blank()) +
theme(axis.text.y = element_text(size = 10, colour ="black", hjust = 0.5, angle = 90))
fig_host_symbiont_tax
#
egger_regression_uni <- rma.mv(yi = Zr, V = VZr, mods = ~sqrt(VZr), random = ~1 |
authors, data = dat)
Supplementary Table 3: Regression coefficients (Estimate), 95% confidence intervals (CIs), variance components (V) and variance examplained, R2[marginal] (R2) from the meta-regression with symbiont_tax_broad.
# getting marginal R2
r2_egger_regression_uni <- R2(egger_regression_uni)
# getting estimates: name does not work for slopes
res_egger_regression_uni <- get_est(egger_regression_uni, mod = "sqrt(VZr)")
# creating a table
tibble(`Fixed effect` = c("Intercept", "sqrt(VZr)"), Estimate = c(res_egger_regression_uni$estimate),
`Lower CI [0.025]` = c(res_egger_regression_uni$lowerCL), `Upper CI [0.975]` = c(res_egger_regression_uni$upperCL),
`V[authors]` = c(egger_regression_uni$sigma2, NA), R2 = c(r2_egger_regression_uni[1],
NA)) %>% kable("html", digits = 3) %>% kable_styling("striped", position = "left")
| Fixed effect | Estimate | Lower CI [0.025] | Upper CI [0.975] | V[authors] | R2 |
|---|---|---|---|---|---|
| Intercept | 0.124 | 0.035 | 0.212 | 0.026 | 0.255 |
| sqrt(VZr) | 1.314 | 0.817 | 1.810 | NA | NA |
pred_egger_regression_uni <- predict.rma(egger_regression_uni)
# plotting
fit_egger_regression_uni <- dat %>% mutate(ymin = pred_egger_regression_uni$ci.lb,
ymax = pred_egger_regression_uni$ci.ub, ymin2 = pred_egger_regression_uni$cr.lb,
ymax2 = pred_egger_regression_uni$cr.ub, pred = pred_egger_regression_uni$pred) %>%
ggplot(aes(x = sqrt(VZr), y = Zr, size = (1/VZr) + 3, )) + geom_point(shape = 21,
fill = "grey90") + # geom_ribbon(aes(ymin = ymin, ymax = ymax), fill = '#0072B2') + # not quite
# sure why this does not work
geom_smooth(aes(y = ymin2), method = "loess", se = FALSE, lty = "dotted", lwd = 0.25,
colour = "#0072B2") + geom_smooth(aes(y = ymax2), method = "loess", se = FALSE,
lty = "dotted", lwd = 0.25, colour = "#0072B2") + geom_smooth(aes(y = ymin),
method = "loess", se = FALSE, lty = "dotted", lwd = 0.25, colour = "#D55E00") +
geom_smooth(aes(y = ymax), method = "loess", se = FALSE, lty = "dotted",
lwd = 0.25, colour = "#D55E00") + geom_smooth(aes(y = pred), method = "loess",
se = FALSE, lty = "dashed", lwd = 0.5, colour = "black") + ylim(-1, 2) +
xlim(0.05, 0.45) + # geom_abline(intercept = mr_host_range_link_ratio$beta[[1]], slope =
# mr_host_range_link_ratio$beta[[2]], alpha = 0.7, linetype = 'dashed', size
# = 0.5) +
labs(x = "sqrt(sampling variance)", y = expression(paste(italic(Zr), " (effect size)")),
size = expression(paste(italic(n), " (# of species)"))) + guides(fill = "none",
colour = "none") + # themses
theme_bw() + theme(legend.position = c(0, 1), legend.justification = c(0, 1)) +
theme(legend.direction = "horizontal") + # theme(legend.background = element_rect(fill = 'white', colour = 'black'))
# +
theme(legend.background = element_blank()) + theme(axis.text.y = element_text(size = 10,
colour = "black", hjust = 0.5, angle = 90))
fit_egger_regression_uni
Much of coding materials have been borrowed from h
sessionInfo() %>% pander()
R version 3.6.0 (2019-04-26)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
locale: en_AU.UTF-8||en_AU.UTF-8||en_AU.UTF-8||C||en_AU.UTF-8||en_AU.UTF-8
attached base packages: stats, graphics, grDevices, utils, datasets, methods and base
other attached packages: plotly(v.4.9.0), ggbeeswarm(v.0.6.0), MCMCglmm(v.2.29), ape(v.5.3), coda(v.0.19-3), metafor(v.2.1-0), Matrix(v.1.2-17), pander(v.0.6.3), magrittr(v.1.5), gridExtra(v.2.3), kableExtra(v.1.1.0), forcats(v.0.4.0), stringr(v.1.4.0), dplyr(v.0.8.1), purrr(v.0.3.2), readr(v.1.3.1), tidyr(v.0.8.3), tibble(v.2.1.3), ggplot2(v.3.2.0) and tidyverse(v.1.2.1)
loaded via a namespace (and not attached): Rcpp(v.1.0.2), lubridate(v.1.7.4), lattice(v.0.20-38), corpcor(v.1.6.9), assertthat(v.0.2.1), digest(v.0.6.20), R6(v.2.4.0), cellranger(v.1.1.0), backports(v.1.1.4), evaluate(v.0.14), highr(v.0.8), httr(v.1.4.0), pillar(v.1.4.2), rlang(v.0.4.0), lazyeval(v.0.2.2), readxl(v.1.3.1), cubature(v.2.0.3), rstudioapi(v.0.10.0-9000), data.table(v.1.12.2), rmarkdown(v.1.13), labeling(v.0.3), webshot(v.0.5.1), htmlwidgets(v.1.3), munsell(v.0.5.0), broom(v.0.5.2), compiler(v.3.6.0), vipor(v.0.4.5), modelr(v.0.1.4), xfun(v.0.7), pkgconfig(v.2.0.2), base64enc(v.0.1-3), htmltools(v.0.3.6), tidyselect(v.0.2.5), tensorA(v.0.36.1), codetools(v.0.2-16), viridisLite(v.0.3.0), crayon(v.1.3.4), withr(v.2.1.2), grid(v.3.6.0), nlme(v.3.1-140), jsonlite(v.1.6), gtable(v.0.3.0), formatR(v.1.6), scales(v.1.0.0), cli(v.1.1.0), stringi(v.1.4.3), xml2(v.1.2.0), generics(v.0.0.2), tools(v.3.6.0), glue(v.1.3.1), beeswarm(v.0.2.3), hms(v.0.4.2), parallel(v.3.6.0), yaml(v.2.2.0), colorspace(v.1.4-1), rvest(v.0.3.4), knitr(v.1.23) and haven(v.2.1.0)